i would love to see it as a scripted FPS, much like the Call of Duty series. then online would be multiplayer/free roam with dozens of maps (oh, imagine the possibilities for all the maps!!!)
there have actually been "skins" for games like battlefiled 1942. this pretty much just cover the graphical aspect, turning the characters into joes/cobras, and the vehicles, etc...
it was never really finished (i think they hit a legal snag with hasbro?), but i think if you try real hard you can download the unfinished version somewhere.
but i really think a new fully licensed game is way overdue, with the power of these current consoles, sky is the limit! you could even have different "skins' for the characters from the cartoons and comics! (similar to what they did for the transformers movie game, including the G1 bot skins)
toggle for lasers or bullets?
