My favorite characters are often the underused ones, as it happens.
Some examples:
The Beast (both X-Men cartoon series, particularly the 90's Fox show)-to many people (including most producers) the X-Men franchise is essentially 'Wolverine and His Friends', but I've always been a fan of Henry McCoy. He's a genius in the body of a big blue gorilla; what's not to like?
I remember initially being stoked that Beast was going to be included in the Fox cartoon show, but alas, Beast rarely (if ever) got a chance to shine on the show. Hank has always been known for being one of the wittiest heroes in the Marvel universe, but on TV he didn't do much more than quote some poets and authors. It would've been cool to see Beast and Iceman hook up and done some shtick in the episode "Cold Comfort", but it was not to be. It didn't help that Beast spent much of the show's first season behind bars.
Beast never even carved a major swath in the live-action movieverse, but given how badly some of the other characters were treated, that might be a good thing.
Moltar (the Space Ghost: Coast to Coast franchise)-Moltar didn't hog the limelight like Space Ghost and Zorak did (though I enjoyed both characters), but I always found his understatements funny. I would have rather seen him on Cartoon Planet instead of Brak; but then, if he had been there, the 2 shows would've been virtually indistinguishable.
Yin (Yin Yang Yo!)-the truly sad thing about my having to put her on this list is because originally, YYY was made to focus on both Yin and Yang in tandem. But now that Toon Disney is on the verge of mutating into Disney XD, the bigwigs behind it have began tageting boys specifically, and so now Yin has begun taking a backseat to Yang, rather than things being equal like before. It's a pity, since Yin has always been my favorite character in the series and I enjoyed the balance a lot more.
Sarah Dubois (The Boondocks)-some of you knew I couldn't make it through a thread like this without mentioning Sarah. I'd really like to see more of Sarah, and not just because I enjoy looking at her. I get that The Boondocks is primarily a black show, and I have no problem with that, but I personally think Sarah has the potential to be a decent counterbalance to her husband Tom's square demeanor--I envision the 2 of them as an interracial Dharma and Greg--so it's a pity that she's such an underused element on the show. Sarah could be so much more than just "the white lady Tom married".