First of all I would like to apologise for the length of this post. This is a small essay on Season 2.
As someone who really enjoyed Ncuti Gatwa's Fifteenth Doctor and will go to bat to defend season 1, I agree that season 2 is much weaker and pulls his run down as a whole. However I think there is one small fix that would make Gatwa's run feel much tighter. Ruby should have remained the main companion.
Belinda's story arc about being stuck with the Doctor and trying to get back to 2025 was hardly a plot for season 2 and more like a bookend for each episode in a much more episodic season. Let's assume for a second that the finale played out mostly as intended, the Poppy storyline would have made much more sense with Ruby in Bel's place. We first met Poppy in season 1 as Captain Poppy in Space Babies and the babies refer to them as "Mummy and Daddy" which was foreshadowing Wish World, and if we take the original ending as potentially still canon Poppy will grow up to be Susan Foreman's mother. If so, it would be much more satisfying for Ruby, who knew about the Doctor's granddaughter from both Maestro and Empire of Death to be the grandmother as opposed to Bel who never learnt about Susan.
Next thing we fix, or at least make a bit more sense is in The Interstellar Song Contest, when the Doctor goes Scorched Earth on Kid and Bel says how "If the Doctor is angry, the world will burn". Even though I contend that this is still out of character for Fifteen, Bel hasn't been with him for nearly enough time to make this claim. Ruby would be near the end of her second year travelling with him and she has already seen him defeat Sutekh, the God of Death at this point.
Another reason why this makes the finale works better with Ruby in Bel's place is that Conrad, the villain actually responsible for the Wish World, was introduced and set up in Lucky Day as Ruby's antagonist. He didn't ever meet Bel in either that episode or The Reality War, thus making her share the Doctor's punishment feel random whereas if it was Ruby, we would two villains; the Rani and Conrad who are personal enemies of the Doctor and Ruby. The only other thing this would need to change is who helps Shirley in Wish World, the two options I would get are either Mel or Anita from the Time Hotel.
So with this change what would it do to the structure of the season? Not much really. Joy to the World still takes place with the Doctor having let Ruby live her life for a year. Then we lose The Robot Revolution since its story is to set up Belinda's "Get me home!' arc and I've taken her out of the season. Instead we move Lucky Day from episode 4 to episode 1 so we see the aftermath of season 1 from the Doctor and Ruby's perspective back-to-back. Then episodes 2, 3, 5, 6, 7, and 8 can take place in the order they do currently. Since we dropped one episode I would place the audio story Sting of the Sasquatch in episode 4's place. I chose this audio original over On Ghost Beach because the plot feels too similar to the Doctor and Bel's arc in Wish World to put it in the same season.
So here is my newly proposed season 2.
Joy to the World
Lucky Day
Lux
The Well
Sting of the Sasquatch
The Story and the Engine
The Interstellar Song Contest
Wish World
The Reality War