I miss the good old days that you're referring to more than you could imagine. In terms of regaining popularity by running Mesa 24/7, I think the words "uphill struggle" would be a massive understatement. So I agree that we'd have to offer something different (like other PS maps, nukes, and time limits as you mentioned). The idea behind the IA custom map rotation was to attract players looking for something other than the same old same old; and it it did work to an extent, but we need to get in there and play in order to keep the games alive.
While I cannot deny that the custom map rotation has been a complete failure thus far, I think more than just the maps are to blame. Organizing practice sessions with open doors to the public would definitely help regain some popularity. I think we need someone to get the troops riled up and remind everyone how much fun Crysis can still be.
To answer your question about what the story will be in Crysis 2, all I can say is that the amount of responses to this topic will serve either as encouragement or doubt for the future.