I'm currently re-watching the original animated series (in the middle of season 3 so far) and although I remembered bits and pieces, it's fair to say that X-Men 97 definitely improved the characterisations of certain characters (though screwed up with Rogue in the early episodes).
In a Season 1 episode, Callisto tried to sexually coerce Cyclops into impregnating her- Definitely would've gone over kids heads but is kind of surprising they actually had that in a Saturday morning kids cartoon.
Cyclops was such a suck up to Xavier- He will literally berate someone for suggesting something that he thinks is a bad idea or a waste of time, yet if Xavier agrees with the person, Cyclops does a complete 180 in attitude and suddenly thinks the idea was good. He also kind of threw a mini temper tantrum over Iceman.
Cyclops and Wolverine have a go at Gambit for seemingly no reason.
Gambit says "The name's Gambit, remember it!" a lot more often than you think, alongside Rogue calling people "Bright Eyes". Therefore the X-Men 97 episode titles "Remember it" and "Bright Eyes" were clues that those particular episodes were going to be Gambit and Rogue heavy respectively.
Jean wore her hair down quite a lot in the early seasons.
Polaris decided to fake her own kidnapping rather than have a break up conversation with Iceman
Gambit and Rogue are in some sort of romantic entanglement. It's not quite boyfriend/girlfriend officially but it's also not strictly platonic since Gambit confessed his love for Rogue and she has kissed him on several occasions with her hand as a barrier.. It's enough to say that Rogue did cheat on Gambit with Magneto in the early episodes of X-Men 97 and that there was no past relationship with Magneto present in the original series.
Morph was able to morph into animals like a rhino and imitated Wolverine's claws whilst in his form. However Wolverine was able to shred Morph's claws with his real ones. This means that Morph turning into characters like Juggernaut and Hulk and using their strength makes sense (because size and strength is relative) but still leaves a question over how he was able to use Quicksilver's superspeed (unless Quicksilver's body makes him very aerodynamic thus allowing superspeed to be possible). It does leave the question of whether Mystique can do the same as Morph since they're both shapeshifters.
Xavier is kind of annoying so I'm glad X-Men 97 used him sparingly
I prefer Rogue's look in the original series compared to X-Men 97
Sinister was more creepy in the original series than he was in X-Men 97
Beast acted unprofessionally with a patient of his and would be classed as abusing a position of trust. He also got very emotionally attached to a sentient spaceship very quickly.
Xavier falls in love with Lilandra very quickly despite the two of them only having a couple of brief conversations.
Bishop was kind of irritating in the original series so X-Men 97 improved his character.
Cable has a son in the future called Tyler so I don't imagine he'd stick around as a main character for too long in X-Men 97.