There's nothing that says what Jean's power limits are. She's crazy. She was a Phoenix bird in one movie and a zombie that disintegrated people in the next. They should redeem what X3 did to Phoenix by expanding her powers even more and showing the audiences she's a "phoenix" because she keeps resurrecting.
Otherwise, the Phoenix we got was just meh
Her powers could have been so great that after Wolverine stabbed her, her mutant power like...just kept her essence afloat. She's a being without a body in The Wolverine. Like maybe by killing her in X3, the Phoenix force was created in a sense. It could re-materialize her body from the flames in DOFP.
Or they could just bring her back with Cyclops in an alternate timeline. But I feel that would make her seem less powerful... they didn't really make her the goddess she should have been. I guess I just want her presence in The Wolverine to be linked to DOFP. But I'm just glad she's back.