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The problem with AJ was that the game was clearly set up for a sequel but because of the negative reception it got, the next game didn't bother following up on any of the dangling plot threads and they shoved Apollo to the side. Still a good game.
His character may have been pushed aside to accommodate Phoenix and newcomer Athena, but Apollo's arc got resolved between the next two games, with more emphasis on him in Spirit of Justice funnily enough.
Remind me what happened to Kristoph's black psyche locks...
Or the fact that Apollo & Trucy still don't know that they're related or that their mother is still alive.
Also, Apollo's arc in dual destinies was essentially retconned in SoJ (which did a far better job of giving him a mentor figure).
Both things that they can come back to at any point. I'll concede that Apollo and Trucy should be wrapped up, but Kristoph's black psyche locks don't need to be; it's meant to represent the fact that Kristoph simply will not indulge in his secret of his own volition. The same goes for Athena in Dual Destinies, which further explains that she doesn't even know the truth and trying to pressure her into it will damage her psyche.
As for DD's backstory for Apollo being in conflict with SoJ's backstory, it really isn't. SoJ's backstory happens first, he has to move away due to things heating up in Ku'rain, then DD's backstory happens later. Now that Apollo's out of the picture for now, Ace Attorney 7 (which is going to be released on the Switch) can focus on Phoenix and Athena, instead of juggling three main characters.
There's really not that much to reveal about black psyche locks at this point. What we've been given from Dual Destinies is about as good as it'll get on the informative side. Kinda like how I'd love to see The Phantom's true identity/who he works for, or the Founder's Orb being used properly, but they are both just left as is.
And that's fine. As it stands though, Phoenix will still be around and playable, just possibly less so in favor of Athena for the next game.