April Stewart shared at a convention once that Wendy's pitch being altered was a decision by Trey Parker, not by herself, and suggested she is capable of performing a voice closer to the original. She also shared on Twitter once that she could perform Ms. Crabtree's voice, though she was killed off before it was used for the show.
So, you're somewhat correct, but the change in writing coincided with the change in voice actresses more by coincidence.
Had Bergman not passed away, she may have altered the voice to suit Trey's wishes.
Oh, easily "Mr. Garrison's Fancy New Vagina" out of the listed options. Not only did Trey nearly quit the show, which says plenty itself, but imo, it says even more that Trey and Matt felt it necessary to not only undo the sex change but to later revisit the issue with a different perspective. Compare how they still refer to some of their oldest episodes as comprehensive and current, like "Chinpokomon".
I also count "Manbearpig", "The China Probrem" and "Raising the Bar" among my least favorite episodes, but I know the latter is fairly popular. Surprised you didn't list "A Million Little Fibers", which I've always had a soft spot for but know most fans loathe.
FYI, I liked season 20, and would only view "Douche and a Danish" from that season as a particularly poor episode, as it does the absolute least to advance the running storyline.
Clyde is a bit of an everykid. He likes comic books and movies like everyone else, and sports. He really wants to be more than just a random kid, but he's not really as capable of being a hero or villain as he wants to be, being easily defeated by Cartman and the boys on both accounts. He's just not a good fighter nor terribly bright.
He's a bit of a jack of all trades, master of none, as I see it - which is both what makes him a great character (he's flexible and can be used for different roles) but also what weakens his character (lack of consistency) compared to say Craig, Tweek, Token or Jimmy, who all sort of own their own traits or gimmicks.
I think it would look like a bad thing, especially if the girl was smaller, UNLESS she had a weapon and therefore posed an immediate danger.
Asking for a fanfic? :P