I don't think this game will make a difference in terms of future Ace Attorney releases; Capcom is working on Edgeworth 2 now, and this crossover is being made by Level 5.
I do think that if they make a non-spinoff game in the main Ace Attorney series, it will probably be a sequel to Apollo Justice, but it will presumably feature Phoenix himself in a prominent role again. I do like that we have the Edgeworth games filling in a bit of the gap between PW3 and AJ, letting us know what was going on with some of the other characters without really interfering with Phoenix's arc. I sort of hope that the next Edgeworth game takes place a bit later and helps to tie the universe together a bit more as well.
Edit: another thought-provoking update:
