I'm gonna go completely off-topic now all of a sudden and briefly discuss an idea I'd had a little bit ago about how to improve the plot of Metroid Prime 3.
Now its plot is fine, pretty solid, but when I got to thinking about it, there's a single element that, in my eyes, would have made it really good.
The short version? Cut Gandrayda and Ghor, keep only Rundas.
To elaborate, they introduce these partner characters into the plot as part of some force to combat the Space Pirates, but we never see them fulfill any potential. Aside from Rundas, but even then only barely. Rundas was easily the most interesting because he actually came to your aid, interacted with you, and seemed to be a cool (heh) guy, only to soon after become a victim of possession and force you to fight him, with one of the most amazing boss themes ever might I add. Gandrayda and Ghor... well, Gandrayda plays a single prank on you but otherwise these two do absolutely nothing to make them interesting.
Cutting them and putting a greater focus on Rundas would have been a great improvement. Have him be present throughout the plot, have him aid Samus more, hell, let them team up in some situations for some neat moments. Then near the very end of the game, he pulls the inevitable heel-turn-via-possession, making the gut punch that much more powerful. After you're forced to defeat him, you're even more motivated to destroy Dark Samus and the hordes of Phaaze. It would've been brilliant.
And please keep the boss battle theme.