Ridley in Prime 1 made me lose more than 2 tanks. He was more fun.
Using the wiimote to mess with levers and things didn't enhance the game in any particular way. It just created a few little extra things to do, which didn't cut it for me. It The only time I felt like they made those additional controls fun was when I had to speed-fix the broken wires on the emergency escape capsule. I feel like overall, the time spent on messing with gimmicks was supposed to make up for the puzzles being relatively pathetic.
The MOST gimmicky, and worse feature for that matter, was Hyper Mode. LAME. I used this as little as possible because it made an easy game even easier. Hyper Mode should not have replaced super missiles and power bombs. I would rather have collected power bomb expansions than ship missile expansions because those were pretty much worthless. At least power bombs let me blow up big glass tubes. Metroid's supposed to be about getting cool items and seeing what you could do with them in the expansive world, not getting lame upgrades that you need to use once or twice to advance ahead.
Being able to play the game like an proper FPS was great, but all the enemies were ridiculously easy to kill, and so were the bosses, even though I consider my aim to be pretty bad with a wiimote. The final showdown with Dark Samus was very disappointing as well. I think Prime 1 was moderately difficult, whereas Prime 2 upped the ante a bit. Prime 3 was just too easy. If I found Prime 2 harder than Prime 1, I don't think it's just me "getting used to" Prime games.
And missiles? Totally worthless. What's the point in having around 250 of them if you barely need them for anything other than seeker missile doors? Ridley alone in Prime 1 justified collecting the majority of missile expansions.
The upgrades were also very disappointing. In Prime 1, I felt pretty pumped every time I got a new upgrade. Varia Suit, Gravity Suit, Phazon suit, wave beam, ice beam, plasma beam, power bomb, super missiles, seeker missiles. In Prime 3, you get upgrades that you don't have much use for later. I had high hopes for beam stacking, but you only get 2 upgrades that are pretty similar to each other. I also thought there would be some cool suit upgrades, but after the PED, which you get at the very beginning of the game, you get the hazard shield which isn't is just a little mod to the PED suit. What gives?
One more thing about Metroid being "isolated". I don't know about that criticism, but Metroid Fusion used Adam, and he was just fine to me. I doubt the federation would've bothered anybody if they weren't so involved with your missions. Usually, they just told you to go do your missions and figure it out yourself. At worst, Fusion told you the general area of where to pick up items. Prime 3 basically made you the Federation's soldier. This isn't Doom 3. Not cool.
Pros: Neat FPS control, better graphics
Cons: Gimmicky controls, low difficulty, not enough cool upgrades and not enough puzzles requiring them, weak music, worlds felt... dead