I think do it in two. Or rather resolve it in two, so the third movie can be coming together.
First movie, X-Men go to space Shi'Ar, that crystal's name I can never remember, some fun cosmic adventure where Jean does go Phoenix (no tease like X2, but this is an actual development in the plot).
Second movie is the Dark Phoenix Saga mostly like it is in the comics, complete with fighting on the Moon, Shi'Ar, etc. Maybe not have Jean kill a planet that is inhabited with billions (TAS made the same change, as it would make Jean irredeemable, and presumably they wouldn't want to end this exactly like TLS).
Third movie is back on earth where the band is getting back together as it were against a new threat (Sinister or Genosha, perhaps?). That way after how dark things got in the last one, the satisfaction is in seeing the team be working together all on the same side again.
Just how I would do it.