Something is missing...
I think you're missing some precussion, and maybe something else to go along with the main part of the track. It seems to lack depth, which can be a bit distracting to someone that wants to use it in a game like Metroid Fusion, because while it should be able to go in the background, it shouldn't be part of the background to the point it blends. Imo, most music that is used for a boss tends to be DnB. This sounds more Ambient, but I'm not saying that's bad. But for a boss like Nightmare, it didn't simply lie in wait just to drain all of Samus' power. It would attack her and switch the Gravity Generator on so it was harder for her to retaliate. Granted, it's not as kill-happy as the SA-X, but it still did some dirty work (unlike a certain vine with the Plasma Beam).
If none of this is making sense, just think of it this way: for a boss like Nightmare, you need to make it feel like the boss is trying to drain you internally, not just externally. This track blends so well with the background it actually sounds peaceful. You don't want peaceful. Bosses are not peaceful, they hit you harder than other enemies after all. It's just missing a certain "air" of darkness, if you will. It needs more depth, which is a goal of most boss tracks. Basically, the track, since most people don't know about how a boss lives, the music helps subtly tell of it. For SA-X, it simply walked during the calming music, but if Samus was ever spotted, the mood changed entirely, and it chased after her very quickly. The music told that story very well: get in my way and you'll perish. Try figuring out Nightmare's mode of destruction, and you'll be able to put that into words, and from there, into music.
If this doesn't help, I'm sorry...I'm a writer by heart. It's just kinda hard for me to be simplistic ^.=.^;