Hmm, I can't decide. I like Nightmare of Nunnally-- perhaps because I'm so fond of Nunnally herself --so I'd definitely be interested in seeing an animated version of that.
On the other hand, it would probably make more sense franchise-wise to go with a different timeline, since that'd be easier to expand on even further if it works out. This could result in an anime prequel, following Charles and Marianne and CC and VV when they were the younger generation, which might be interesting. I might prefer something set far in the future or far in the past, though, involving a new cast entirely-- and given Sunrise's inclination to keep adding characters to the franchise, and the way they've handled Gundam over the years, they may prefer something like that.
On the other hand, we don't actually know that it will be an anime, or even a TV anime. It could be a movie remake (a la Evangelion) or a new manga or video game or just about anything.
What would I prefer? Something well-made. Pretty much any of these ideas has potential, if done with a bit of care.