I have a little conspiracy theory. I think Belinda was never supposed to exist.
So, I believe that Ruby was supposed to be a companion for two seasons. I think they had fair notice, probably before they started filming the first, but I think the general storylines were already put in place, and major episodes, specifically 'Robot Revolution', 'The Well' & 'Interstellar Song Contest' were already largely drafted.
I didn't dislike Ruby as a companion, but I really did quite love Belinda. But I feel like this ending feels matched with Ruby's themes, as well as the FINAL episode basically fridge Belinda, literally trapping her in Stepford before having her literally locked in a box.
Final episodes, especially Companion final episodes always involve the active companion. Especially in an RTD season. Rose becomes the Bad Wolf/gets locked in an alternate dimension. Martha walks the entirety of the earth to unionise the human race. Donna unlocks the metacrisis. Even in Steven Moffat, Amy brings back the Doctor, Clara jumps into his timestream, Clara basically drives both the season 8 and 9 finale two parters.
Belinda does... Very little, comparatively. Even her moments with the Doctor feel strange, there's no fallout of her calling the Rani's forces on him, not even any fallout to them being married. She gets a scene where she runs off into the woods to scream, but she doesn't even get an explanation as to who Poppy is from Space Babies, and how the Doctor knows her.
Comparatively, Ruby not only has the emotional weight of stopping Conrad, she also convinces the Doctor of Poppy's existence. Hell, Belinda isn't even THERE when they give the God of Dreams and Wishes to Ruby's family for them to raise.
Theory. Alan Budd was Conrad. Ruby was Belinda. Season 2 starts with a flashback of her kissing Alan, noticeably sexist and disrespectful, names a star after her, and we cut to seventeen years later. The MissBelindaChandra Bots, now known as the 'MissRubySunday Bots' grab her and take her away. The Doctor, of course, comes chasing after her, and the two reunite. This also answers the question as to how Mrs Flood is both Ruby's and Belinda's neighbour. They're the same character. It should be the same house.
The season, largely, continues as normal. Ruby and the Doctor have very much the same dynamic as Belinda and the Doctor. They probably rewrote a lot of the dialogue for a more combative dynamic to distinguish the two. But generally, the two are pretty close, best friends, dressing up and goofing off, and on a rewatch, even when Belinda's words are her own, her actions never feel far from Ruby's.
(I'll admit that's a stretch as 'companion' characters tend to have the same actions, but I hope you understand what I mean.)
Season 2, the vindicator isn't a thing. Ruby admits to enjoying life with the Doctor, and they commit to a couple of funky trips. Replace the 'something is connecting us' speech with Belinda with something like 'the whole universe, and I found you twice/Doctor, I thought I might have to live my life without you, without the universe, let's go everywhere'. This even helps the moment where the Doctor promises Rose that she Will see him again seem to make a lot more sense. Bear in mind, Joy To The World still takes place, so he still has his 'missing Ruby, making two coffees' arc.
(This opening would probably be a parallel to Partners In Crime in some senses? The Doctor and Ruby in the start of Robot Revolution being like the Doctor and Donna constantly missing each other.)
Here, the vindicator never existed. Anyways, it's never mentioned more than a couple of mentions per episode, and even as the deus ex machine weapon against Omega, you could remove every mention of it from the season and it would be fine. The Doctor and Ruby don't have any pressure on getting back on time, they're vibing. It is very much like the last season, only replace the Susan Twist cameos with Mrs Flood cameos.
In 'The Well' we get an indicator that the human race is not in fact gucci. And in 'Interstellar Song Contest' Graham Norton pops up and tells them that the Earth was destroyed on the 24th of May. And this is like Journey's End, when the Doctor and Donna return to Earth, and then the planet vanishes.
(I really see a LOT of Donna's era in this season)
So, in Wish World, the Doctor and Ruby are married. Replace the scene where Ruby knocks on the door and says everything is fake with Ruby being the Doctor's wife telling him that she doesn't remember their daughter. Keep the scene of her being asked about giving birth to Poppy and screaming in the woods, keep the scene of her finding Shirley, only this time, someone else calls the police on both the Doctor AND Ruby. Which is why we get zero fallout of the Doctor feeling like he can't trust Belinda. Because here, they were BOTH reported and taken in.
So in Reality War, Ruby is the companion confronts Conrad, except it isn't Conrad in this version. It's Allan. Noticeably sexist Allan. Belinda even says 'all you ever did was correct me' and that's what he's doing. Correcting the World, in his image. His obsession with obedience.
Hell, it even makes Poppy make more sense. Poppy is born because 'Allan' would want 'Ruby' to be a mother, and in season 1, we see Ruby ask the Doctor if he has children, to which he responds that he will have. Ruby sees him with the space babies. And RUBY, who remembers Poppy, tells the Doctor NO, that she was real, that Poppy existed and he NEEDS to save her. Ruby even tells Poppy 'I wish we were (your parents)' which would make space babies make sense.
Maybe the Zero Box exists, maybe it doesn't, but midnight hits and it's the 25th. And Ruby convinces everyone as to Poppy's existence, and the Doctor leaves, pours regeneration energy into the time vortex, bringing Poppy back and entrusting her to Ruby. (Poppy returns, but is fully human.)
This works for Ruby's themes way stronger. Ruby's arc was always about finding her mother, and being a foundling. I mean, she was even wiped from existence. (They try to make Belinda relate with being trapped in a time storm which is weak).
This is RUBY'S story. Even the idea around family, we get wonderful moments with Cherry and Carla, and after a whole season of Belinda nattering about her parents, we only see her mum for three seconds. And I think they wrote Lucky Day to establish Conrad, and explain why Ruby matters to him.
I don't think this makes the season bad at all. I am a bit upset that Belinda seems like such an afterthought as a character. But here's my theory all the same.