Conker - for a former 2nd Party Nintendo character who had such a legendary game on the n64, he's surprisingly getting very low support, even after Banjo Kazooie got in. There has been some support for the guy on Twitter recently but still not as much as the other two popular Microsoft characters, which I personally find it criminal.
Adeleine - One of the most memorable and even important characters from one of the main Nintendo series, Kirby, who originated in its 64 entry. I guess she's overshadowed by Bandana Waddle Dee's popularity and fan demand. What's even more shameful is that she didn't even get any sort of representation in any Smash game for unknown reasons.
Duke Nukem - One of the most legendary FPS characters that influenced the genre, along with Doom, Wolfenstein and Quake, and has a surprisingly good history with Nintendo. My take is that he's overshadowed by Doomguy, and while I do want both, I do find that quite a shame for the king.
Nights - the lovable genderless SEGA character, who was even created by the same guy behind Sonic. the original Nights game is certainly a cult classic, and I'm sure there are many people who fondly remember it (Shingeru Miyamoto even said it was the only game he regrets not making), sadly Nights support is almost non-existent.
Scorpion (or any other MK character) - one of the most revolutionary Fighting game series that's specially known for its extreme gory violence, that's even banned in Japan, and well I guess that's the tip of the Iceberg. however, with all fairness I think a Mortal Kombat character is one of those M-rated guys that can be toned down and still stay somewhat true to its series, not every MK was M-rated and I mean if Ridley can use his skewer than I don't see any reason why Scorpion shouldn't be able to use his spear thingy. As long as there's no blood it's fine, I guess.