Word of warning: Take what I have to say with a few grains of salt, because I have no idea what I'm talking about from any standpoint.
The choirs seems a bit muddied at times, such as at the beginning (~0:04), like playing two (or more) notes at the same time and making a sound that isn't really clear and doesn't know what it wants to be. The choir also gets kind of boring after the first minute or so. If you can bring out the sound, diversify it somehow, and make it all around seem more natural, then it would sound much more intersting, imo.
Overall, I can hear the source Brinstar stuff, but I don't think it's adding a whole lot to the mix. I feel like it's playing second fiddle to the choir and lead instead of having an equal part. It doesn't sound like there's enough bass in the mix, so if you kicked the bass on the source up a notch, maybe brought something to the lower end of the bass spectrum, then you can make it better.
I like what you have going on from 2:07 to 2:56. I don't know if this is what you were going for, but it seems like it wants to be all one section, but it got broken into three parts: 2:07-2:23, 2:23-2:39, 2:39-2:56. As a whole, it could be improved by making it truly one section instead of three pieces trying to be one section. The original stuff you added is good, but I feel it dwarfs the source material, while at the same time like it wants to bring some MP into the mix; Maybe incorporate Chozo Ruins with this section instead of the end?
On the ending: You could cut out the Chozo Ruins bit at the end, and nothing would be lost from the mix. It's cool that it's there, but it doesn't add anything, as if it's there just to be there. You could end the song at 4:21, too (before cutting the CR bit out), because the next 10 seconds don't really fit in any spectacular way. The fade out could probably do with being a second or two shorter, as well.
Overall, it's a good mix, but it's not awesome.