I'd like to see:
Scorpion with Sub-Zero as an echo
Morrigan (does she still count, since she wasn't the poster girl during the first Darkstalkers game)
Chun-Li
Dr. Eggman
Morrigan is an oddball, cause she is supposed to be one of the normal heroes of the story anyway. Even during Darkstalkers one. The thing that happened is she overtook Demetri severely, compared to just being more of a notable other Hero like Luigi is. Demetri got sidelined severely. Could be somewhat compared to how Toad is. A notable hero too, but just lesser, but one people still care about. Introducing Jedah, another vampire, didn't help.
The OVA had Morrigan and Demetri as the core heroes, and they're part of the major villain set in the cartoon too. It seems like the idea was they were designed to be on equal grounds first, and then Morrigan overtook him severely. Albeit, the heroes were hijacked entirely by another character(he does this in the OVA, and somewhat in the cartoon too. The cartoon also had issues that it didn't have a straight hero who fights. Just a bunch of good guys on the same side. It also did many characters dirty, but Pyron became an outright wimp in it. Morrigan being based upon the more traditional demons was more annoying than doing her dirty, though tying her to a King Arthur character came out of nowhere and was just a bad excuse plot for an episode).
Anyway, the rest are much more accurate to your point. Scorpion still remains to be a main hero or villain in any normal game or adaption, same with Sub-Zero. They certainly both have played heroic and villain roles, sure. Well, there is Scorpion's Revenge, but it's kind of an awkward thing where there's multiple major characters, and it's still not a main game series. It doesn't help MK changes the main character a lot, so you have ones like Shujinko who are in the same status as Liu Kang. Main Characters.