-Wall o' text-
You hit the nail on the head. When I was younger and played Metroid Prime a lot, I almost didn't like the first one. I found almost to dry in terms of story telling, kind of like they dropped you in the middle of no where and kind of forced you to find your way around without any story telling. Except for those annoying little pop-ups telling you where to go and what to do next, I almost found Prime 1 aimless and boring.
However, this was a while ago and on when I played through it again, I really got a grasp on how awesome of a game it was. There was an intense story there, you just had to take some initiative to find it. Where MP2 and MP3 were extremely polished and almost glossy in some parts, MP1 was rugged and real.
It's almost the same thing as Fusion, Fusion was a great game, but the whole computer thing telling you where to go and what to do almost ruined the whole thing. The game definitely didn't have the real gritty Metroid feel of the original and Super Metroid, that's for sure. Not to mention that it could be beaten in under an hour.
In conclusion, I really felt like all three of the primes were epicly different games. Each had a special feel to their own that could each be liked or disliked. Prime 1 was a survival/investigation type game, with a type of hidden story that wasn't glossed over. Prime 2 was somewhat similar to Prime 1, except for completely different. The aim of the game was basically the type of game it was: Fix a problem with a systematic approach. And finally, Prime 3 was definitely a finish-the-fight type dealy. Unfortunately, this game was almost Halo.