Metroid Prime 3 was the first in the trilogy to be made for the Wii rather than the Gamecube, so there’s some motion controls like thrusting the nunchuck to launch the Hook Shot, and operating levers/contraptions by rotating the Wiimote clockwise and thrusting forward. The point-and-shoot controls were then backported into the first 2 games in the Metroid Prime Trilogy release on the Wii.
I’ve read/seen some reviews that claim that Samus starts the game with all her equipment collected from the previous game. Although Samus usually does start these games fully powered up, then quickly loses her powers for plot convenience; you start the game with limited powers for no explained reason. Sure, she has the morph ball with the basic bombs, and can charge the default beam weapon, but you need to find the missiles. The likes of Super Missile, and morph ball Power Bomb don’t even feature in the game. The likes of Spider Ball and Screw Attack come much later in the game.
The overall feel of the game is different. First of all there’s voice acting - but Samus is still a silent protagonist. Early on, you see plenty of space marines, and a few bounty hunter allies which makes a change from the isolation in the other games. After a few chapters, Samus does become more isolated but is guided by an AI. Some scenes feel like they have taken influence from other franchises like Star Wars or Halo. In the early game, it’s nice to experience the wider universe since it's not just a desolate world with a few creatures, but then I’m not sure it feels like the same series.
It’s a weird start to the game with Samus on her ship and you can interact with a few devices by pointing and pressing buttons. However, most of this is just a gimmick - you only really need to interact with the main button to choose a destination. When on the Galactic Federation ship, you are interacting with switches in a similar way, pulling switches and twisting them using motion controls. . The button to talk (A) is the same button as shoot, so it’s easy to shoot because you aren’t quite close enough for it to register. The prologue seems to give a misleading impression of what the game is like, although the first couple of planets you visit are very linear.
I think the linearity is a response to complaints about Metroid Prime 2 being a bit aimless, but maybe they went a bit overboard because not only is it linear, you are told exactly where to go by the AI. As you progress through the game, it does open up to larger worlds and more freedom to explore. When you are used to the hand-holding, it’s a bit confusing when the game eases off and tells you to go to a room but you can’t quite reach it because you don’t have the power-up yet. From that point on, you often are led to an obstruction and then it’s up to you to further explore in order to get the next upgrade and come back.
You now have a minimap on the HUD which is an obvious, and much needed feature (It was definitely needed in the previous game). You will still go to the map to see the larger picture, but it does help you orientate in the world.
As part of the story, Samus ends up being corrupted by phazon and is given a new suit to harness the power. You basically go into “hypermode” at the cost of 1 energy tank and can quickly destroy enemies. Sometimes it's necessary as some enemies have resistance to all-but-Phazon. Other times it's just entering easy mode. Another criticism of the previous game was the bullet-sponge enemies. Now the enemies are much easier to defeat and the inclusion of the hypermode makes some enemies a little too easy. Most of the bosses require you to shoot certain weak-points then eventually have to use hypermode when the true weak-point is exposed.
Metroid Prime 2 was a chore to play when you had to constantly switch between Dark Beam and Light Beam. They have simplified the beams and missiles so that they basically stack. When you unlock the Ice Missile upgrade, this can open the White coloured doors but also the doors that require a missile.
The amount of backtracking is reduced, although there are still a few tedious sections. The previous 2 games have had a “key hunt” before you can reach the final boss. In this game, there’s 9 energy cells but you acquire half of them as you progress through the story. They are used to open doors on a spacecraft, and if you choose all the doors on the critical path, then you don’t need all of them. Personally, I was one cell short so had to backtrack out of there, visit a planet, go through several rooms, pick up the cell, backtrack out of there, and retrace my steps on the spacecraft. Then when you have completed your objective, there didn’t seem to be a shortcut out, so I had to backtrack out again. Then you have to go to a certain room, interact with a computer, and backtrack out of there.
An idea that has reduced the backtracking is that there are several points on the map where you can land your ship (and you can call it to land remotely). This means there are several routes off the planet when you do need to leave, and you can cut down the amount of backtracking when you do land again. Your ship also allows you to save the game and replenish your energy and missiles, although there are a few save stations around as well.
When you die, sometimes you restart at a checkpoint rather than your last save station which definitely alleviates the frustration when you haven’t saved in a while.
I criticised the previous game for the backtracking, unclear directions, bullet sponge enemies, lack of freedom to explore (well, being penalised by having so many gates that require a power-up that you don’t have). These have been addressed but maybe too extreme. The series did need some streamlining but it’s a bit too watered down in the early game. Additionally, it's the easiest game in the series, but follows the hardest game. There’s still challenging moments for sure, and maybe it will be harder if you haven’t played the first 2 games. However, it will feel a bit stripped down for returning players. In my opinion, it is far better than Metroid Prime 2, but doesn’t quite live up to Metroid Prime 1.