The thing is that had no idea about the Keys while I was going through the game. So I probably missed several, I am following a guide on where to go, I have found Several so far.
The thing I don't like about Prime 2 is the exploring, it doesn't feel as fun to run around grabbing the keys as it did the 12 Artifacts in Prime 1, I guess because prime 1's environments are more interesting... These ones are kinda dull, as the whole Light/Dark thing was popular at the time, so they made Prime 2 a little more gritty looking.
Also, the Ammo system for the different beams, I don't see what the point of that was.
EDIT: Just beat Prime 2, even got the bonus ending thing where she takes her armor off before entering her ship. I got 87% of the items, which is good. Beat it in 11 hours, and 28 minutes, a lot less than what I though I beat it in. I was expecting... 20 Hours. Boy, was I off. XD
But to summarize my feelings on Prime 2, amazing game just like the first one, not as good as the first Prime, but still great.
So Metroid Prime Trilogy is amazing, the only negative I see is that some of the flare from Prime 1 is missing, like the water actually rippling realistically when you shoot it, now its just a 2d splash effect, and when you charge the ice beam, ice doesn't freeze over the gun like it did in the original, and I have no idea if they took out any tiny details in Prime 2, and I doubt they would in prime 3. But yeah, amazing game.