Let's see...
Morph and whatever the fuck they turned it into. Oh, and the forced romance with Wolverine.
Wolverine in general. He was just...sorta there and ineffectual. Except for going off, feeling lonely, and romancing fucking Morph.
Storm suddenly turning into a wet dishrag and fucking off to do some weird romance introspection thing with Forge (who they also fucked over).
Gambit getting cucked, and despite going out like a total boss, died thinking Rogue decided to be with Magneto despite the literal YEARS he'd spent dedicated to her.
Xavier in space - that whole thing, and how his return was handled.
Beast...was Beast in this? I think he was. He must have been...oh yeah, he drove a sentinel for a minute. And tried to romance that reporter bitch who turned out to be a terminator. He sure had memorable role. I'm sure he said "Oh dear" or something a few times.
Rogue x Magneto (don't even get me fucking started). And they censored her. A lot. Her whole character was basically ruined.
Now...Cyclops...wasn't bad. His "intro scene" was pretty badass. But honestly...after that he's just Cyclops again.
Nightcrawler was criminally underutilized (as usual). Swashbuckling was terrific, though.
Jubilee was kinda ok. Mojo-world-Jubes was cool, but forcing her pairing with Sunspot for that episode felt like a forced way to get him involved in the story. It would have been a lot better if it was her solo, or even better, with one of the other, older X-Men that knew fuck-all about video games. Storm would have been a fantastic twist, and hey! No powers anymore so she could have had a lot of time on her hands to try out gaming.
The whole show was essentially : "Muh nostalgia except now with more diversity." And yeah, I know X-Men is supposed to include that shit, but this was overdone and felt really forced for the purpose of virtue signalling (as usual).
I probably forgot some shit, but that's just a defense mechanism from my brain trying to block it out as much as possible. I certainly didn't keep it after watching it so I can't go back and reference it.
Edit : Whoops, completely forgot Jean 1 and Jean 2. Eh...can't say I disliked how the Goblin Queen story was done, all things considered.
Really one of the biggest problems with the show is how many out-of-character things the characters did.