Now that I can understand. There are definitely similarities, but it's still Metroid for me, and it's pretty hard for Metroid to transition from the blazing swiftness of 2d Metroid to 3d. A lot of classic franchises have that problem, and I fail to see how they'd be able to fix that, Prime or not. It's extremely difficult to make an actually challenging 3d platformer due to the way they're made, which is why most 3d platformers are more about "how do I get there?", memorization rather than emphasizing reflexes. And it isn't like 2d Metroid ever had challenging platforming to begin with, especially with abilities like the screw attack. It wasn't recently until 3d platformers started to mix 2d grassroots in their gameplay enabling a more agile and smooth experience as we saw with titles such as the Mario Galaxy games. I'd like to see the Prime formula revisited with a more modern twist for a better gameplay experience.
I'm not exactly sure how a 3d Metroid would even work the way people want it. The series is about exploration, secrets, backtracking while still keeping a cool, fast pace. With 3d, that's extremely hard to pull off. 2d, by virtue of its medium, will always be faster.
RE: puzzle-based bosses. Hit the weak point is definitely lame.
RE: Lock-on. I somewhat agree with this.
Funnily, the best 3d example I can think of a fast-paced game with exploration and backtracking is Ninja Gaiden 1.