I have some ideas:
"House of Mouse" (they could have done a lot with this show)
"Captain N: the Game Master" (they could have at least included "Super Mario Bros.", one of the most popular video game franchises of all-time)
"Beetle Juice" (they probably did all they possibly can, but the show could have much more potential, it was decent, but not good enough to follow a classic movie)
"Spaceballs: the Animated Series" (they could have done so much better with this show)
"Looney Tunes" (there are many ideas that I can think of that would have made great episodes, but unfortunately, there cannot be any more new episodes)
"Tiny Toon Adventures" (this show is a classic, but it could have had some improvements, though I cannot think of any right now)
"Gumby" (they had many blockheads on the show, so all of them could have met to take out Gumby and his friends)
"Care Bears" (the villains could have teamed up to take out the Care Bears)
"Teenage Mutant Ninja Turtles" (they probably did all they can with this show, and do not get me wrong, it is a classic, but I personally feel that they could have done more with this show, I do not know what specifically, but maybe more things with the villains, and maybe making more mutant heroes, as well)
"The Legend of Zelda" (there were not enough episodes, they had much material to make more episodes)
These are all I can think of right now, but I will post if I come up with anything else.
Looneytunes/Disneytoons