To be fair, Marvel's 1990s continuity was strong at times (when handled correctly, like the FOX Spidey/X-Men crossover, and Iron Man's apperance in The Hulk)
But yeah, it's been a struggle for Marvel to keep anything afloat. And the quality of their shows varies. This is of course, is why Timm's DCAU was superior, it's run EXACTLY like DC would be run, with a team of writers and an established direction. Marvel don't have that because they want their shows to be self-contained.
Their best show, the FOX Spider-Man series, was developed by Stan Lee, Avrad, and Semper, but Semper was the head writer for the entire run, and wrote a clear and precise direction that went from points A to B. (Avrad got in the way and told him to put Hobgoblin before Green Goblin and other nonsense, which drove Semper from Marvel). That series ended on a cliffhanger, yet nobody would noticed because of the way the finale was written, you could kind of figure where Spidey was going.
The scheduling of CN betrayed and buried Fantastic Four (nevermind that the show itself is the pits), I dont know WHO Marvel piss off, but it might have to do a lot with toysales and merchandising. The Evolution line bombed big time, and the FF one never got really started.