Adjusting to the controls took very little time, but if a sequel is made, I hope their hardon for the Wiimote subsides.
I don't mind the game being Wii-remote only, but my one gripe with controls is how they handled the Grapple Beam. They used a "switch" mentality rather than a "hold" mentality as pretty much every other Metroid game has done, which screwed me up a few times. Further, initiating it requires first-person view, while there are a few times (mainly in the lava area) where keeping the Wii remote in that position will botch your landing.
I have mixed feelings about item authorization. It works for anything potentially destructive. Samus is joining a military operation, so she has to play by their rules. They regulate weapons, as any organized outfit should. And you certainly don't want to accidentally Power Bomb a survivor, or even a corpse that could have given you clues. But the Varia Suit, Gravity Suit, and Space Jump? They have ZERO destructive potential. It makes no sense with them. And shouldn't the Ice Beam be considered Samus's equivalent to the GF freeze gun? Adam authorizes that for all troops when they're deployed, yet leaves Samus with the regular Power Beam.
But I can't really lay all of that at Adam's feet. Recall, the only things Samus ever deactivated on Adam's say-so were Bombs, Missiles, and Power Bombs. In other words, she of her own accord, was taking a pretty minimalist approach even before meeting with Adam, using no Ice/Wave/Plasma Beam, no Space Jump, no Screw Attack, no Varia/Gravity Suit, no Speed Booster, no Super Missile, and no Grapple Beam (although to be fair the opportunity for that one didn't really come up). The one appearance of the playable Zero Suit falls into the same vein here; there was no necessity. Apparently Samus just likes treating life-or-death situations as training, or something.
Majorly spoilerific story comments:
[spoiler]We could have stood some more specific closure as to the traitor. It seems to be James, who got his at the hands of the Metroid Queen (the "missing" soldier would be the one that the game showed being tossed into lava with no witnesses).
But then, wasn't a shot fired while Adam was in the command room? Yet when Samus retrieves his helmet, the flashback simply shows him running off in response to Samus meeting Melissa. This is after that gunshot, so what happened that both Adam and his attacker walked away? Further, Melissa herself met with a GF soldier. But if James previously tried to kill her...what was going on?
I'm also sensing some SERIOUS conflict of canon between this game and the existing Metroid continuity, especially Prime 3. Other M clearly treats Mother Brain as not simply controlling the Metroids but the leader of all Pirates. MP3, however, while it did not specifically reference Mother Brain, pretty much beat the player over the head with Aurora Unit references, including the Space Pirates capturing an Aurora which then functioned as a boss, and images of an "Aurora complex" that was very obviously Tourian. The clear implication is that Mother Brain is in the same boat. Further there are Space Pirate logs referencing a Pirate Command, and, if the Pirates cannot function without Mother Brain leading them, how could they have possibly resuscitated her after the original Metroid? And why exactly does Other M treat the Space Pirates as being synonymous with Zebesians? Zebes was a Chozo settling ground, to say nothing of Samus's freaking home, before the Pirates ever arrived there. By the same token I find it difficult to believe that the Pirates survived the loss of Zebes once, but couldn't survive it again. Why would any race capable of inter-planetary travel go extinct from the loss of one planet?
While it may not mesh perfectly with the series, the game on its own has a pretty great story. I especially loved Ridley's appearance in this game. Was epic in every sense, seeing Samus in shock, watching a rare instance where a "partner" tries to cover for her. I was actually relieved at finding Anthony alive at the end; I felt a lot of sympathy for him. I do kinda wish that something more could have been done about the GF jerks who actually supported the whole Bioweapon project, but I guess leaving them at large is kind of necessary for the lead-in to Fusion.
The ending of the game seems give the impression that this is a story first and a game second. It's awkward that the "true" story is not revealed until after Queen Metroid, the last real fight before the credits. And I use that term loosely, because she's a joke. The only thing remotely challenging about her is dealing with the swarm of her kids; once that's done, she's cake. Phantoon was much tougher, although the "extra" final boss being a rehash who authority-wise falls well below Ridley doesn't make the biggest bang in the world. Was awesome nonetheless, though, I just feel that the game lacks a properly climactic final battle.[/spoiler]