I never understood why Tolwyn hated Blair so much.

I think I'm using cartoony differently than you're reading it; it's not so much that it looks literally like a cartoon as that it has the broad qualities of one... heroes that are universally good, thoroughly evil villains, stories without moral grey areas, goofy friendly aliens, designs based on looking cool over a shared aesthetic and so on.
Also Wing Commander II feels a lot less cartoony when you're playing it. For a long time I had only looked at the game through screenshots and thought that the ships looked cel-shaded, but when I actually played it again I was surprised how much it felt like the later 3D games.
Wing Commander 2 is actually my favorite of the series as far as combat, ship design, and character design goes.

Wing Commander 4 I think has the best story to me and still to this day looks like it could be a pretty top shelf Sci-Fi TV show, even though the game is like 25 years old. The combat in four did leave a lot to be desired and I'm hoping that is worked out with the fan remake.

As far as the four main games go I actually think three is my least favorite by far, for much of the reasons we've already talked about in this thread. I was not a fan of how the characters and the story was handled as a whole, even though I did enjoy the ending. Also i know Chris was never happy with the puppets, but I thought the kilrathi looked pretty good for the time and still hold up decently well today. I was also not a huge fan of the ship designs in three. I know this is a bit controversial but I actually prefer the fan made game called the darkest Dawn which covers the events of three from another Pilot's perspective more so than 3 itself.