I played through this game from start to finish. So, containing the spoilers...
Here's my take.
Visuals
The game has definitively better visuals than the previous two; just as soon as I finished playing this I felt like loading up the original Metroid Prime (from 2002 for Gamecube) and I can say that the game engine has enjoyed some definitive improvements.
-It uses bloom lighting and has a considerably clearer textures
-Its 16:9 presentation provides WAY more screen space; Samus' visor doesn't feel crammed with information any more
-The detail of the textures is much higher than the Gamecube because the Wii does, in fact have more horsepower than the Gamecube, despite what some would tell you
-The range of lighting isn't quite "high dynamic range" but it does give you a huge range of environments; the interesting glow effects of the Space Pirate stronghold are especially interesting. It may force you to properly recalibrate your TV (My advice is to throw a DVD in the DVD player with the Lucasfilm/THX Optimizer and fix your settings) and THEN fiddle with the in-game settings to get it just right.
-To address one of Rob's comments: the Metroid Prime games have ALWAYS had really dark, dark rooms where you can barely see where you are going, especially the first one, so that's really nothing new...
-The Scan Visor interface continues to evolve, making it much easier to tell what you can scan and what you can't, what you've missed, etc.
-One caveat; I find the use of the map has actually taken a step backwards from its predecessors, as it is often hard to navigate the map with the new control layout vs. the old controller scheme; the geography is also more complex meaning you can sometimes have a hard time seeing where you're going on the map.
-It would have been nice if they could have figured out how to get the game to do anisotropic filtering at the very least; the ATI chipset is more than capable of this and it would be nice if the floor and walls didn't get blurry after a few feet's distance. HD it's not, but it's better than the Gamecube's or PS2's visuals.
Audio
The game has a top-notch sound mix, as Rob noted. One of the reasons I bought a Gamecube way back when was because I read all about Dolby Pro Logic II on Dolby's web site and it noted that the Gamecube was the first console to adopt Pro Logic II audio in real-time; since then it's become standard. Nintendo continues to have excellent sound, whether you're going for stereo or surround.
Retro's sound mix is fantastic and immersive, and the music is well-done; especially the music of the Space Pirate stronghold, which takes cues from Metroid: Zero Mission's Pirate themes.
Controls
I don't think I could say more about the controls than Rob already has; I concur that the control scheme is the best of any game for the Wii. If other shooters adopt this style, we're in for a treat.
One thing that is subtle but fun as well is the improved controls for the Morph Ball; moving around on Spider Ball tracks is more fluid now, and you pull your Remote "up" to make the ball jump; this means that some of those wicked bomb jump and ball jump tricks in dark crevices to find that last missile expansion are quite interesting.
The introduction of multiple grapple beam modes, culminating in the "Hyper Grapple" upgrade, which lets you grab certain enemies and then either A) overload them with phazon or B) suck the life out of them, THEN rip them limb-from-limb with a hefty yank of the Nunchuk are a neat innovation.
Storyline
Prior to the game's release, I downloaded Super Metroid for Virtual Console and played through and 100%'d that baby for the first time ever. I was already a big fan of Metroid: Fusion and Metroid: Zero Mission for GBA and I enjoyed the classic Metroid. This gave me a bit of grounding in "Metroid lore".
Some comments:
-The Aurora Units in the game (big brain-like biocomputers) are a very obvious fleshing out of Mother Brain, which dated back to the original Metroid game; Samus' mission is to destroy the Mother Brain in the pirate base on Zebes in the classic story.
-In your final boss battle with Dark Samus you must face a powered-up, mutated AU which very much resembles the battle with the new Mother Brain at the end of Super Metroid
-I disagree with the comment that the game has been "Halo'd" ; it reminds me of the comments that the upcoming Warhammer MMORPG is stealing ideas from Blizzard when, in fact, many things that Blizzard has produced over the years have borrowed concepts from or paid homage to the classic Warhammer universes. In much the same way, I have to argue that the Galactic Federation, giant super-brain-computers, evil spacefaring raiders bent on wholesale destruction and superhero space-battle-armor-clad "bounty hunters" etc. are things that Metroid did first. The Federation troopers DO resemble the Halo guys somewhat, but then again, they're all just a spin on Imperial Stormtroopers anyways, non? If we had to argue about that all day we'd get nowhere.
To address Rob's comments, though, I think that an element of why it sort of feels different from previous Metroid adventures is because it IS different from them; the bulk of the game isn't a one-soldier infiltration mission, and you take the heroine of the series and put her in other environments, like on starships or bases full of friendly soldiers under attack and it naturally feels different. If anything, I thought it felt at times like a superhero movie, because Samus wasn't the only hero, and ends up having to fight her comerades once they become corrupted by her nemesis/evil "phazon twin" Dark Samus. There was also the fact that the hints the game provides (which typically had taken the form of "strange sensor readings" on the other side of the world that your ship's computer were picking up in the previous games) have nicely been incorporated into transmissions from the flagship, and others, which reminded me of the narrative style of Metroid Fusion.
On that same bent, it also started to feel like the Star Wars prequels in the sense that we already know the end of the story and the Metroid Prime series is a prequel series to Metroid II, Super Metroid and Metroid Fusion. Therefore, the story had to be resolved without adding even more things that "don't exist" in the earlier-made games that take place later in time (sound like Star Wars yet?) and make sure that they don't come back or at the least, don't come back until much later (e.g. if they made a game that takes place AFTER Metroid Fusion does.)
I feel that this is par for the course with prequels. The story wasn't truly original, true, but no one was really expecting it to be. I think it served its purpose and it threw in some neat cues to the other games across the entire Metroid universe.
Other gameplay elements and criticisms
Having the weapons take on the character of the weapons from the classic games was a neat touch; now your blaster types "stack" like in the good old days; and just as in Fusion, you get ice missiles.
Two things I am critical of though, are that you really have no way of using all your missiles later in the game; the charge combos of Metroid Prime are missed in that regard. On that same note, through the mission you collect a total of 11 missiles for your gunship, however, at no point do you ever need them. The most missiles you ever use at once is a whopping 2 or 3, to destroy obstacles. The others are just pointless pickups to get 100% of all pickups to get the "secret ending" clip, a tradition in Metroid.
The gunship has two additional elements you can activate: a blast shield and you can bring the ship's weapons online. At no time to you USE these features, implying that these were gameplay elements that they took out of the game before its release, and the game wants for them. Also, the lack of multiplayer ALSO feels like something taken out of the game before release; we have 4 bounty hunter characters with unique powers, a la Metroid Prime Hunters, and it feels like the game was MEANT to have them face off in "training deathmatches" etc. completely separate to and complimentary to the main adventure. So these features are missing in action.
Finally, the bonus features such as the soundtrack and concept art are unlockable with tokens you earn in the game by scanning monsters, beating bosses, or pulling off tricks. The most valuable of these tokens are the green ones, which you can only USE by 'e-mailing' them to someone else you know that also has the game on their console if they're in your Wii's address book. Given that the game has no multiplayer, this feels stupid; especially if you don't personally know anyone else with a Wii AND the game to get the last few widgets and add-on bonus features, like starship bumper stickers.
Conclusion
I would have given the game 9 out of 10. It aint perfect but it's sweet. I'd also argue that NONE of the Metroid games are worthy of a perfect score in their own right, dating back over 20 years!
If you have a Wii, this is the OTHER game besides Zelda that you "must" own. And if you've played other Metroid games, play it on Veteran mode the FIRST time through and challenge yourself.
I can only hope that they make another game like this, maybe a remake of the misadventure on SR388, the homeworld of the Metroids, tying it into the Prime series. Time will tell. In any case, other game developers should learn from Nintendo's FPS/platforming control scheme.