Yeah, Samus is pretty busted on her own. But she has a lot of DNA/Phazon in her like you said. What if there was a way to make that breakdown? I like how fusion gave her the metroid's weakness based on their DNA. Maybe there could be a nother weakness exploit like that?
I really want to have a bad guy that could fight her on equal footing, without it being a parasite or generic dark form with super powers.
She's free of Phazon, it was neutralized when she destroyed Dark Samus/Metroid Prime and the Aurora Unit. As was her Metroid-element when she merged with the SA-X. If anything, she's now just the *good* parts of X/Metroid since their weaknesses are gone as of Fusion (Metroids/Ice, respectively). Its kind of hard to say *what* she is by the end of Fusion because at that point she's Human + Chozo + Metroid + X, by the end of Metroid 5 I wouldn't be surprised if she's part-Ridley.
There *are* bad guys that fight her on equal footing. The thing is they are usually much larger than she is or empowered in some fashion (Ridley, Craid, Quadraxis, Ing Emperor, Metroid Prime, Omega and Queen Metroids, etc).
Within the lore-universe of Metroid, I don't think anything on her scale can actually pose much of a threat to her. Consider that her most dangerous enemy was herself be that Dark Samus or SA-X, the bounty hunters she runs across in the Hunters or Prime 3 are easily dispatched by her even when they are empowered and corrupted by Dark Samus+Phazon. The shadow-bad guy for Prime of Sylux doesn't even dare fight her directly.
That said, we've never seen a Chozo warrior in their prime in the series, so maybe they actually would pose a threat to her. But then these same warriors failed to deal with the Metroids, and she (in this very game) re-enacts Terminator 1 on 40-some Sarah Connors.