Why do areas seen in Pikmin 1 change so much when there seen again Pikmin 2?
Great question! This is something that bothered me for quite a long time. The areas Olimar visits in Pikmin 1, with the exception of the Forest Navel, return as three of the four areas in Pikmin 2. I will use gifs gracefully provided by @somasoa to demonstrate this!
In Pikmin 2, the Forest of Hope has become the Awakening Wood:
"The interior of this hemisphere contains a chip coded with charts detailing a new region. I explored this forest the last time I was here, but it's clear that it has undergone some dramatic changes. The plants and animals have also evolved significantly. I've given this forest a new name... The Awakening Wood. I must begin to form a hypothesis to explain why the forest changed so rapidly."
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Playable Character in Pikmin 2, August 2004]
The Distant Spring has become the Perplexing Pool:
"I've recently noted that changes in this planet's environment happen at a very rapid pace. Compared to how it was when I was here before, the Perplexing Pool has changed drastically. Due to frequent tectonic shifts, the region appears slightly different each time I enter it. It could be a natural phenomenon, but it's as if I feel the presence of a guiding hand. ...Maybe it's just my imagination running wild."
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Playable Character in Pikmin 2, August 2004]
An artificial swimming pool set with tiles was constructed [at the Distant Spring]. "It looks as though a lot of time has passed…"
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
And the Impact Site and the Final Trial have collided to become the Wistful Wild:
"I've never tasted a nut quite like this. It's difficult to explain, but it tastes like...sorrow.
PS: I can't shake the feeling that I've been here before. Aha! This must be the exact spot where I crash-landed last time!"
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Playable Character in Pikmin 2, August 2004]
We've seen many different types of creatures, as well as the incredible speed at which they evolve and diversify. "Look closely… It's the same place!"
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
The natural cycles of the PNF-404's surface sometimes appear to accelerate at monumental speeds. As Olimar mentions there are frequent shifts in the tectonic plates. While in Pikmin 2 PNF-404's continents resemble Earth as we know it, the tectonics have shifted so much by the time of Pikmin 3 that the Pangaea Proxima supercontinent, which shouldn’t occur for another 200 million years, seemingly formed in the span of a few years at most.
"There were large-scale tectonic movements that shifted the relative positions of the continents."
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
Until very recently, I couldn't quite think of a logical explanation, but I had two leading theories:
This theory posits that the "warp speed" travel used by the leaders in the Pikmin games to cross lightyears of distance in an instant has an impact on how those travelling through space perceive time. In essence, this theory would mean that while from Olimar's perspective only a day or so passes between Pikmin 1 and Pikmin 2, for PNF-404 several years pass.
While this theory sounds promising at first, it quickly falls apart when considering other factors. If years were passing on PNF-404, years would also be passing on Hocotate - Olimar would have been missing for far longer than just a month by the time he returned home, and his family (his wife, his two young children and dog Bulbie) would have aged significantly. There's also the fact that in Pikmin 2, Olimar leaves PNF-404 after collecting enough treasure to repay the debt owed by Hocotate Freight, only to realise he left Louie behind and immediately return with the Hocotate Freight President. The time between Olimar leaving Louie behind and returning to PNF-404 in Pikmin 2 is the same length of time (if not longer due to the gold plating the S.S. Dolphin first model, or “Hocotate Ship” as it is also called, received) between his first escape from the planet in Pikmin 1 and his initial return with Louie in Pikmin 2, yet the planet does not change between both Pikmin 2 expeditions.
This idea also certainly doesn't explain the extent to which the the continents move between Pikmin 2 and Pikmin 3 while the species living on PNF-404 appear to remain extant.
Theory #2: Human Meddling
This theory proposes that humans still live on PNF-404, explaining the pristine condition of several human items and structures, such as the Hero's Hideaway in Pikmin 4, and continue to inhabit the planet just out of sight. This could serve as an explanation for the "guiding hand" Olimar felt changing the Distant Spring into the Perplexing Pool:
"[The areas aren’t] exactly the same, but we intentionally made them look similar to give a sense of déjà vu that you’ve been here before… Like maybe it is the same places, but time has passed and humans have interacted with them…"
[Source: Shigefumi Hino & Masamichi Abe, Directors of Pikmin 2, Nintendo Dream Magazine, May 2004]
However, this theory similarly falls apart when considering that the Leaders we see in the Pikmin games are, in fact, humans who left PNF-404 to colonise other planets over 2000 galactic years ago - so long ago that over the generations the humans forgot where they truly came from. 21st century human food, technology and structures could not exist on PNF-404 after they had been gone for so long.
"The planet where Pikmin live is a mysterious one that shows a different side of itself with every visit, but this time players arrive in an age with the strongest traces of past civilizations. You'll be seeing plenty of familiar things that will help you feel closer to Pikmin than ever before."
[Source: Yutaka Hiramuki, Planning Director of Pikmin 4, Nintendo Co., Ltd., July 2023]
With this in mind, we may start to get closer to the actual answer - and it explains how so many people crash on PNF-404 in the first place.
As we know from caves, there appears to be a distortion in the space-time continuum surrounding the planet. Time in the interiors of certain caves on PNF-404, likely due to a powerful magnetic impacting special relativity or gravity, passes more quickly compared to time on the planet's surface.
"Because of a powerful magnetic field deep under the surface, time does not pass underground. When you climb back to the surface, you will return at the exact moment in time that you entered the hole. Time will not have passed."
[Source: Exploring Underground: Above Ground, Page 25, Instruction Booklet of Pikmin 2, August 2004]
"I calculated the difference. It looks as if about 1/6 as much time passes on the surface as you spent underground. Time seems to move differently in the underground spaces on this planet… I’m not sure how it works, but I suppose that means you can take as much time as you need to explore caves."
[Source: Collin, Member of the Rescue Corps and Comms Operator, Non-Player Character in Pikmin 4, July 2023]
"Subterranean Time Warp
Upon returning to the surface after exploring underground, I noticed the hands of my clock had barely moved at all, and I had been down there for hours! I can only assume that on this planet, time flows differently on the surface than it does underground."
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Playable Character in Pikmin 4, July 2023]
"The dilation of time can be observed when traveling at speeds close to the speed of light or while in the vicinity of a massive gravitational field. Perhaps the entrance leading to the cave is some kind of wormhole, which then connects to a different pocket of space-time..?"
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Pikmin Garden, Nintendo Co., Ltd. website]
Not only does this apply to time in caves, but also to the layouts of the caves themselves:
"The powerful magnetic field between the surface and underground can have peculiar, unexpected effects. You can't rely merely on your memory, as familiar areas can often appear foreign. Just focus on gathering all of the treasures, and you'll be all right."
[Source: Exploring Underground: Subterranean Q & A, Page 26, Instruction Booklet of Pikmin 2, August 2004]
"Despite entering the same cave, it seems that the layout inside may change."
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
"If there are two entrances above ground, the location of the exit will change depending on which one was used as the entrance. They look like they're in the same locations, but there are slight differences due to the phase of space-time."
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
And this also appears to extend to the surface of the planet, being the reason for some of the differences we see between Pikmin 1 and Pikmin 2:
"Case 2
The position and designs of the [landing site] circles may vary even when visiting the same areas. Maybe the space-time continuum of this planet is warped...?"
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
"While exploring this warped land, I got the feeling that time passed faster than usual. Upon researching it further, I realized it was just my mind playing tricks on me. But whenever I touch this object I can feel the space-time continuum bending!"
[Source: Captain Olimar, Employee of Hocotate Freight and Captain of the S.S. Dolphin, Playable Character in Pikmin 2, August 2004]
But that still leaves the mystery of what specifically is causing the alterations in the planet's space-time.
Theory #3: PNF-404 Is Alive
It's been highlighted on several occasions that a mysterious force other than gravity appears to draw ships in and cause them to crash when approaching the planet.
"I still can't shake this awful feeling that there was something more to our crash than we know... It felt almost as if some power from the planet's surface was manipulating our ship..."
[Source: Alph, Koppaite Scientist and Engineer of the S.S. Drake, Playable Character in Pikmin 3, July 2013]
"When we came in for our landing on this planet, I definitely felt like we were being pulled in by some sort of mysterious power. It clearly felt different than your typical planetary gravitational pull. I just can't seem to shake this feeling. What could it have been...?"
[Source: Alph, Koppaite Scientist and Engineer of the S.S. Drake, Playable Character in Pikmin 3, July 2013]
Paradoxically, it seems that only the spaceships capable of leaving the planet are the ones that crash in the first place. Perhaps there is some mysterious force or will at work that wishes to keep visitors to the planet in place.
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
The planet seems to change every time you visit, and it's not uncommon for the same place to look completely different.
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
Unlike the space-time continuum that we're familiar with, it's speculated that the planetary phase is shifted into a different time period each time someone crash-lands observes the planet.
With these changes, it's almost as if the planet itself has a will of its own.
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
According to a certain theory, planets themselves meet the definition of a living being. Could it be the planet itself that is calling out to us with some purpose in mind? It could then be conceivable that everything we experience on this planet is being manipulated to further that very purpose.
[Source: Chet, Mihaman Scientist and Research Task Force Lead, Pikmin Garden, Nintendo Co., Ltd. website]
All of this seems to suggest that PNF-404 misses the humans that left it behind and has recreated elements from its past, such as human artefacts, fruit and so on in an attempt to lure them back there. If the planet only changes phases when it's being observed by outsiders, this explains why it changes between Pikmin 1 and Pikmin 2 but doesn't change when Olimar left Louie behind in Pikmin 2 - Louie was still observing it in the latter, keeping it in the same “planetary phase”.
This would also be what's happening in caves, just on a smaller scale. Every time a leader enters a cave, its phase shifts, giving it a completely different layout.
In short, to answer your original question, the planet PNF-404 is alive and shifts phases every time it is observed by outsider. This is why the areas change so much between Pikmin 1 and Pikmin 2.