In the distant future, I'd love to see a coop game as well. But I think it should probably jettison the geoscape entirely because large-scale base management just doesn't work very well in coop.
Each player could be given a set number of soldiers that are automatically replaced when others die, and the players choose a series of missions that are available for them. There could even be in-mission things that propel things along -- picking up weapons leads to their being researched, performance can determine finances for equipping units, rescue and other missions could have special rewards.
The player would essentially be like a force commander rather than commander of Phalanx. He'd be in charge of a single unit and he could even deploy that unit in any coop (ie - it wouldn't necessarily always have to be the same coop players, each player brings his unit to a particular battle). It would only be a sub-game of the existing game, but it'd give the player the soldier leveling, a coop battlescape, development of technology/threat over time, and more flexibility which can be good for coop games where scheduling isn't always easy.
Just a little proposal to throw out there. But I don't think it would happen any time soon.