Job 24: Mega Man
I'd think that Mega Man would fall into the category of "a character whose absence would long be questioned due to how popular and iconic they are to the series" - from what I recall, that was the initial reaction to his absence from Marvel vs. Capcom 3, so I think he would count.
Mega Man's moveset in Marvel vs. Capcom 2 was fairly bare-bones, from what I recall, but Smash Bros. shows that he can work well in a fighting game setting and that he has plenty of options for melee attacks.
Hyper Combo ideas (assuming we're supposed to include these - if not, then ignore this section)
1. Beat Plane - Beat hovers by Mega Man, assisting with his attacks where each of Beat's actions depend on what you press. (Light = Beat charges, Medium = bullets, Heavy = bombs)
2. Double Gear System - a utility super where time is briefly slowed down and Mega Man's attacks are powered up. However, this uses up all of his super bars, with the effect lasting longer depending on how many super bars are consumed. (to prevent it from being spammed)
3. Super Adaptor - Mega Man fuses with Rush, gaining
the Super Armour from Mega Man 7. In this state, he can fly freely and shoot out powerful rocket fists, though he can't use any of his other Hyper Combos in this state.