Interesting pitch (I know you messaged me about it before posting in this club too) that I like a few parts of. Such as bringing lots of characters back I like. The biggest issue I see here though is that I don't think you can kill off characters like Kristoph and Godot without backlash from fans as they were well-developed characters. (Maybe not as much remorse for Kristoph since his evil plot reveals what a villain he was, but at the very least: Godot was a prosecutor I think most people liked).
"The Phantom" concept is very similar to Blackquill (which I commented before elsewhere), but perhaps this isn't the worst thing in the world - it might still come as unexpected to a lot of the audience playing the game.
For the next Ace Attorney game, we need a subplot that would captivate players more then Dual Destinies, DGS, and Spirit of Justice. What better way to do that then to bring everyone together for one grand finale. I don't mean the end of Ace Attorney, I don't want it to ever end. But I do mean the end of Phoenix Wright. Let's face it, his entire existence in the franchise now is to get the games to sell, and doesn't offer anything new. So, here's my idea:
There is a criminal organisation who break convicted murderers out of prison, and recruit them as a part of their organisation. Detective Gumshoe has been working undercover with the organisation, hence why he hasn't been seen in a while. Eventually, the Wright Anything Agency get involved, and recruit Godot to help expose them (I know Godot's in jail, but that's what interests the organisation in the first place). While they get involved with the group, both Kristoph and Godot are killed on an assignment, and Phoenix Wright is the defendant. In one final trial for him before his retirement, he defends himself while Athena does investigations. Eventually, it's revealed that "Godot" was actually the phantom, and the real Godot was locked up by the organisation.