The same problem occurred with Bunnie Rabbot in Sonic Satam. A cool cyborg with a unique dynamic, but remained a background character and a Faux Action Girl for 75% of the show. The comics make a little more use of her, but not that much.
Is this along the lines of They Wasted a Perfectly Good Character discussions?
I adore PJ from Goof Troop. For whatever reason, he's just not as popular as his pal Max. He isn't disliked, and most fans are sympathetic to him, but I've seen precious few say they love him. I can understand this because while Max is "normal", PJ's specific quirks are highly relatable if and only if you're an introvert with nervous issues, which may be why most of the people I have seen say love him (myself included) obsessively write character analyses for decades-old cartoon characters...
On Total Drama, I never understood why Eva didn't become an Ensemble Dark Horse. She seemed to have just as much potential as Noah, but no one seems to care about her.
edited 30th Jan '14 10:24:57 PM by PPPSSC
Who ironically was wasted potential herself due to Flanderizing her to her positive aspects, and spending most of her time as a predictable Straight Man to Sonic rather than getting much valid Character Development.
I feel like Dana Tan from Batman Beyond got shafted both by the show and by portions of the fanbase. She was a character that didn't really have any counterpart in Bruce's supporting cast, the girlfriend who predated the event that spurred the main character to become Batman. Terry having to choose between his relationship with her and Batman could've been more poignant than Bruce and any of his love interests, because Dana had history that the others didn't. She also could've been a "normal person" viewpoint, a contrast to Bruce, who was still Batman at heart, and Max, who was very gung-ho and eager to get into the superheroing. But in the show she never had a role beyond being Terry's main social life, either showing them having carefree fun or, increasingly more often, showing the strain on his social life by having her angry at him. And then some of the fans ignore all the positives of the relationship and talk about Dana as if all she did was nag at Terry, which is just really unfair. At least the show's creative team realized that they had short-changed her, even if they never got around to fixing that.
I love Tiana from The Princess And The Frog. Many people forget about her in favor of Charlotte and that sucks. I was surprised to find out she's a very underrated princess.
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I never thought negatively of Dana, but I do think she was underused for pretty much the reasons you stated. I did like her role in "Epilogue" of Justice League Unlimited.

What I mean is, characters who are pretty damn awesome in whatever series they're in, but always ignored in favor of another character(s), or just characters who don't get enough props. My example: Cyborg, from Teen Titans. Now, I'm not saying Robin (the one who is definitely more popular) is overrated or anything like that, as I do genuinely like him as a character. My only problem is that fans often seem to forget Cyborg exists in favor of talking about Beast Boy and Raven or Robin and Starfire. Honestly, Cyborg is, well... A GODDAMN CYBORG. He shoots lasers from his hands, destroyed Brother Blood, and is basically a living Sci-fi smartphone! The epitome of badassery! Why the lack of love?
THE BEES! THE BEES!