Batman
The one and only Batman.  There's been a few for Mugen already, but in my opinion none of the Capcom-styled ones have reached greatness.

Booker DeWitt
Booker DeWitt is the protagonist of Bioshock Infinite.  His gameplay could revolve around guns, Skyhook, and Vigor powers.  Perhaps Elizabeth could help by opening a Tear mid-fight.

Brock Samson
Brock is the ultra-badass bodyguard of the Venture family.  Brutality is the name of the game, whether it be his trusty combat knife or with his bare hands.

Bryan Fury
Everyone's favorite undead cop from Tekken.  Personal favorite character in the franchise.  I prefer his Tekken 5 attire, but that would be up to Sean.

Conker
The foul-mouthed, womanizing, booze-swilling, dope-smoking squirrel from Conker's Bad Fur Day. 

Daryl Dixon
Walking Dead's redneck with a heart of gold.  Specialties include his trusty crossbow and his combat knife when things get up close and personal.  Biggest problem with him would be a voice actor.

Heisenberg
Sean already mentioned a few of his potential moves that we talked about.  Not sure which outfit to go with.  I dunno if I'd rather see him in his tightie-whities or his fedora-sporting Heisenberg wear.  Could potentiall be a problem with his voice acting as well.

Jason Vorhees
Crystal Lake's true son, the machete-wielding maniac psuedo-zombie.  Tons of potential with him, as he likes to kill people with whatever's laying around.

Joel
The Last of Us is probably my GOTY, and Joel here is a big reason for that.  Guns, shivs, molotov cocktails, machetes, pipes with scissors taped to them, and a shit-ton of other weapons are at his disposal.

The Joker
Like Batman, there's been a few Jokers for Mugen already, but unfortunately they've all left something to be desired.  I'd like something akin to his appearance in Injustice or the Arkham games, as I like the darker versions of him.

Judge Dredd
The no-bullshit Judge from Mega City with a chin that goes for days.  Makes Batman look like a Democrat.

Link
IMO, the Link's that have been released so far are decent, but somewhat lacking in the sprite department. 

Lobo
Buyog's version is decent, especially for it's time, but I think Sean could make a badass version of the Main Man.

Randy Savage
The Macho Man is quite possibly my favorite wrestler of all time.  I would love to see him Mugenized, although the voice may be a problem.

Rocket Raccoon
R.R. would be mainly based off his MVC3 incarnation, as there's good source material to work with.  Plus I'm a big fan of GotG, and I love this furry little bastard.

Spike Spiegel
Spike comes from one of my all-time favorite animes, Cowboy Bebop.  He's a lightning-fast bounty hunter who specializes in Jeet Kune Do and his pistol, the Jericho 941.

Super Skrull
I think Capcom got it right by adding him to MVC3 instead of any of the F4 protags.  4 characters in one, and like RR has plenty of source material.