I wouldn't want to see Alternative animated. A lot of the awe I felt from that game was because of all the previous loops you play through and noticing the differences and simularities.
Sure they could capture the intensity of the fight for survival against the BETA but I doubt they could get the same attachment to the characters as the games.
That's just my two cents.
If anything, I want to see another Muv-Luv game that focuses on...