I was going to call you a blasphemer for suggesting the Prime games are flawed, but I can actually respect or even agree with nearly everything you said...
The key fetching isn't so bad in the first one; I just think they should have introduced that plot element as soon as you arrive on Tallon IV, as it's kind of annoying that you have to go a fair way through the game before you're made aware of this search you could have been undertaking from the beginning...
The keys to get to the final boss in Prime 2 are entirely unnecessary; the game already has substantial length, especially when you consider how tedious it is to more around...
For me there isn't any part of Prime 3 that feels particularly un-Metroid so much as the game as a whole feels un-Metroid...
The soundtrack, with some exceptions, sounds like it belongs in a completely different game and the loss of the sense of isolation is quite unfortunate...
Have a nice day...
Essay Pro