I think UMvC3 isn't ready as it has no (new) ladies. So, with the exception of one of my votes, here we go.
5. Megaman, any version from any Megaman series (save Megaman Zero, but that's technically not Megaman)
I'm personally fine without him in (as in, I can deal with it), but still... about the most convincing thing I've heard on this whole ordeal went something along the lines of, "It's not that Capcom owes it to us to put him in, it's that Capcom owes it to Megaman." That's probably my opinion as well, but it's their game...
I'm partial to Volnutt, he was a blast to play in Tatsunoko, but seriously, pick any version, and I'm a happy fan.
3. Akane Houdzuki, Gyakuten Saiban: Yomigaeru Gyakuten (tied for third)
Okay, sorry 'bout this one, but since Phoenix Wright is in the game, I just gotta shout out to my favorite character in the series thus far. Think her English name is Emma, and thankfully, she's got a decent chance of making it through an alternate DLC costume pack? I dunno, but throwing chemicals around makes more sense than... finger lasers. ^^;
I was so close to giving this spot to someone in Sengoku Basara, but my fandom is greater here.
3. Saki Omokane, Quiz Nanairo Dreams (tied for third)
Okay, left-field pick, I know, but she's cool and she's from an obscure game not many people have played, and to me, that puts her near the top of my list. She was also my main in the little I played Tatsunoko Vs. Capcom, not that I was any good at that game...
2. Sara, Breath of Fire
Breath of Fire represent! You gotta have a dragon transformation, but there's already someone named Ryu in the game... I was close to giving this spot to Fou-lu from Breath of Fire 4, but I have a thing for lesser known characters (and lesser known series), so I'm going with Ryu's sister from Breath of Fire 1, the only lady in the series to demonstrate the ability to turn into a dragon.
1. Akira Kazama, Justice High School series
I dunno about you, but I needs me some Justice High School, and she's seriously the best character in the series. She was also slated for a playable crossover appearance before that game got canned, so here's a good chance to pick it up. Powered, Pure Rider, or both with a DLC pack, you just can't go wrong.
Honorable Mentions: Keiji Maeda (Sengoku Basara), Jubilee (X-Men)