Phoenix and Dark Phoenix is worse than Wolverine/Akuma because it's so easy to fix the latter two with patches. You really only need to do a few things to do it: reduce Wolverine's overall damage, reduce Akuma's invincibility on Tatsu, take away the damage boost of Berserker Charge to make it only boost speed, and make Berserker Slash not invincible. I don't even know where to start with Dark Phoenix because nearly everything about her is a bad design decision. Reduce damage, reduce speed, reduce chip damage on feathers, reduce teleport speed, reduce life gained from Healing Field, reduce meter gained by Dark Phoenix, and nerf X-Factor and you're left with a character that's still pretty ****ing ridiculous. Wolverine and Akuma also don't decide games by themselves. I've never seen someone completely outplay their opponent only for Wolverine to make a comeback by himself the same way Phoenix does. Same with Akuma,
except for that one time.
I don't see how this is like Fox and Marth at all. Those characters both had matchups where they were at a disadvantage or could go even with characters. They were very dominant against most of the cast, but that's the way it usually is in poorly balanced games like Smash.