I just saw on neoseeker.com, an easier way to do it. it says:
"...The next stage of the battle will entail you fight a floating head(This will be deja-vu for anyone thats played Metroid Prime 2:Echoes). All you have to do is get behind it and shoot the shiny red spot, simple right...? WRONG!!! It floats around and above you, so you lose your lock-on when you try to dash around it(Frustrating...I know). What you do is shoot the mouth when it opens up, before it fires 1 big-az shot at you; or you could shoot this box-like thing that pops out from the bottom, before it shoots a blast at the floor to make a shockwave. The main attack you should watch out for is the attack that shoots 4 gold beams out in random directions. Oh, and to make this battle alittle harder...you can't regain any health during the last phase of the battle, you only get health back at the beginning of the floating head battle and thats it. Good Luck! Your going to need it!"
This was submitted by a guy named Ryuvayne, it seems a bit easier than what I said. also you might want to make a copy of you're game file because after you defeat it, if you press yes to start the game again you can't go back. so either back up your data or get 100% of the items or else. if u want to see the link i got this from its from here:
http://www.neoseeker.com/Games/cheats/Wii/metroid_prime_3.html
hope it helps,
animeoverlord1