I have played three Pokémon Mystery Dungeon games and no matter how simple the story I always end up crying. Weird how attached one can get to characters. But it seems to be more so when they aren't human.
I could get so attached to the characters because I use hacks to play as whatever I want. Never anything overpowered, I just use it to play as Pokémon from my team from the main RPGs.
I feel you. I feel like Mystery Dungeon especially benefited from coming out around the time that both Pokemon and the translations of Nintendo’s games started getting pretty fun (the SomethingAwful member that was on the localization team, etc). The Gamecube and GBA/DS era in general was a time when things really tended to get creative, even if it didn’t always work out, and PMD was definitely one of those times where it worked out.
It wouldn’t surprise me if PMD’s simplicity (sort of) is its greatest strength storywise, though. It might not delve into a lot of complex themes and whatnot (it’s not like Tales of which might go into human vs elf racism or fantasy world politics or the effects of war and the like), but the relentless focus (ideally) on you and your partner is always what I feel the game did strongest.
I’ve said this before, I think, but I remember a survey once done in both Japan and the US where people were asked what they thought of when they heard Pokemon, and while JP mostly answered Pikachu, US answered “Ash and Pikachu”, which made someone (Tajiri, I think?) feel that the US understood the teamwork theme of the franchise a bit better. I’m not even sure if that was really a thing that happened since my memory’s fuzzy, but I think PMD has something similar going on. Since it’s you and your partner, the focus is entirely on the two of you supporting each other and getting through all sorts of adventures, which makes for a very strong emotional investment.
Also this is unrelated but I’m rather curious to hear about the PMD hacking scene again! Last I heard the custom portraits thing took a zillion years to get right because the games are pretty fragile code-wise, heheh.