Been playing Metroid Prime: Trilogy on PrimeHack (a Dolphin emulator fork that was designed for this purpose.) I finished Prime 1 and 2, but 3 is giving me some issues on account of the motion controls.
After re-mapping, the controls to (mostly) standard FPS controls on a gamepad from the default Wiimote controls (and in defiance of the original GameCube controls,) I have to say that it was a fun experience and a reminder of simpler times.
Something that threw me off and that I had to relearn was that spamming the trigger wasn't the best way to deal damage - as a Metroid game, taking the time to charge up your weapons got you better results. This, honestly, was a fun way the game stood out from more traditional first-person games in the genre.
Much of my good times with the games was when they were like that, actually. Understanding that they were both a Metroid Game and an FPS: a hybrid of the two, taking and mixing elements from both.
When I first started playing the trilogy again, complaints about backtracking in other games were fresh in my mind. Playing through the games again made me realize that the Prime games managed to get it right. You would often be moving back through areas you've already been in, but when you did, it would be with new equipment that let you solve problems differently than the first time you went through. Or it would tease you with things you couldn't do yet but might be able to in the future.
For example, there was an area in the game that would normally require you to platform through a bunch of monsters and crumbling obstacles the first time through, coupled with a section where you'd have to crawl under some plating to get to the other side of a high wall. Later on, I got some abilities that just let me use grapple points to just swing through areas I'd have to slog through, and a double-jump that let me leap over the high wall.
They even went the extra mile and changed enemy spawns when you returned to certain locations: these weren't random or anything (or I don't think so at least,) but playing through the game normally, it was appreciated and helped the areas from feeling too stale.
Though, I still had some complaints about the game a few years later, after the nostalgia goggles wore off. One was that the games sometimes forgot they were a Metroid-FPS hybrid. Sometimes it included abilities and weapons from the 2D Sidescrollers that worked great there, and not so much in 3D. Prime was good about remembering that, but Prime 2 had some points where it tried to cram those in, and it made some enemy encounters very much unfun.
In addition, there were some points where the progression was a bit unclear. Normally, most of the things you needed to progress a section were in that section, which fed logically into one another. Then once you were done, you'd leave, continuing onto the next, or going back to older sections with your new toys to see what you could do now. However, there were times in the games where you'd have to stop what you were doing in one section, go back to a previous section, get something to progress, and then go back to where you once were and start over.
The game does have a setting where if you don't know where to go next, you can toggle it so you'll get an automated message telling you where you need to go. Though, it seems a bit of a clunky solution to me, and one that could have been fixed with some better design.
Outside the game, emulation itself gave me a couple of problems. Nothing game-breaking, just annoying. Like my crosshairs would always end up listing one way or the other at all times, or when I selected one of the games in the trilogy, I would see a purple screen flash briefly. The game would also start to lag heavily when I brought up a map with a lot of stuff on it, or occasionally otherwise. Didn't stick around - like I said, more annoying than anything.
Though, even with all that in mind, I'm enjoying my time with the game, which has aged gracefully.