My game?
Well, it would be a spin-off of the X series. Since the "Elf Wars" has been described as an event that takes place over the course of an undefined moment at the end of the Maverick Wars, and then takes place over the course of a 4 year span before Weil and Omega are dealt with, that could be enough of a window to explore exactly what kind of tragic conflict eventually made it so that 90% of Reploids and 60% of Humans were all wiped out.
My ideal way of exploring that? By adapting Rockman X to the "Gundam Vs." engine, and making for a nice arcade-style, arena action game, not too much unlike Virtual ON. You'd still deal with Boss Mavericks at the end of a level/map, but in just a different context. And you'd have to fight your way through a bunch of their peons in a series of fights, before you'd get the "right" to fight them, and steal their abilities/Cyber Elves for yourself.
And of course, X and Zero would be a part of this (and would be the high-cost, high-reward units to deploy in the Gundam Vs. style of play). But the desperate times would call for more players to join the fight (and make for more different play styles). If ever was a good time to bring the likes of Dynamo, and the cool peeps from Command Mission back, this would certainly be a good time. Hell, since most of these characters are probably going to meet their unfortunate demises by the end of all this, you might as well have a "Create-a-Char" option too.
Seeing how well Capcom has utilized the Gundam Vs. engine thus far, and is going to use again, in the upcoming Sengoku BASARA Battle Heroes on PSP, I'd like to see what they could do, utilizing the venerable Rockman brand, instead. And besides, people have been clamoring for some way to make a Rockman multiplayer/Vs. game, and well, this is one idea I could certainly get behind.
Besides, I'm sure Capcom also would like to be able to craft such a game that would be able to use the engine, without having to share profits with Bamco (due to the Gundam license).