Phoenix isn't going anywhere. And I'm personally happy with that, but I agree that preferably he should have a secondary role. Him being playable from time to time it's okay and I don't think that's bad at all, in fact that could help the story they want to tell, if it's well executed.
What I'm not really sure it's if they're going to push Athena again. I feel like they might just introduce a new main character to push alongside Nick, with Athena relegated to a secondary role again, which would suck for her.
But yeah Phoenix is going to be around no matter what. The only scenario I could see him not being in a mainline game would be if the series starts selling a lot more, so they're less afraid of getting rid of Nick, and if they have an almost equally popular main character in their hands. Apollo is quite popular but not enough, at least for them, to getting rid of Nick.
And even if we got a new guy that ends being super popular, Phoenix is still the mascot/face of the series. Outsiders to the series don't think of Apollo or Athena when they think of Ace Attorney.
It doesn't help I guess that the games have his name in the title, so folks inevitably associate the series with him. Like, I have known quite a lot of people that haven't played the games calling the series just "Phoenix Wright", some of them didn't even remember the actual name is "Ace Attorney"