Idk, you only really have to scan anything that's red. All of the orange stuff just gives you additional backstory. I thought the backstory in Prime 2 was actually pretty cool. Really all of the lore in all three games is great if you can find yourself getting into it.
The key hunts aren't as bad on replays as they are the first time. Most of them can be obtained as you're playing through the game, if you know where they are. I think that they should have given you access to the clues sooner, so that you could get started on collecting them sooner, though I guess you still can if you notice the spots in which they are hidden.
I think the main reason why I like Prime 1 the best is simply because it came first so a lot about it was new, but I still like Prime 2 a lot. It has a lot of good points going for it, which have just about all been pointed out already.
@Zero I think Prime 1 and 2 are about the same size in terms of area, but it took me less time to complete 2 and I think it's simply because I was already so used to its mechanics.
@Hero_Of_Hyrule I find it very interesting to hear you talk about moving around in Prime 2's world is smoother process over 1, as I felt the exact opposite. For me, Prime 2's world felt a lot more separated, there were less entryways from area to area, and it could also be tough to tell from the maps if you have to travel through an area from the light or dark side. It felt like it took a long time to get across the world in 2, whereas the world in 1 is one of the best-designed worlds I've seen. There are lots of passages and ways to get from area to area, and traversal is generally easy-breezy. It felt like a faster-paced game to me.
I say that because getting from one side of an area to the other isn't the linear progression of hallways that would sometimes occur in Metroid Prime. Progression and map design are more circular, while Prime's progression consisted more of straight lines that you would have to trace and retrace.
Like, when I went to the sunken ship in Prime 1 only to find that I had to turn back, I had to make a loop around the whole world just to get back to the ledge I jumped down from to reach the ship. I reached the roadblock, redid all the platforming I just completed, and went through a bunch of rooms I'd already explored but could not cross quickly. And this is compounded in places like the Space Pirate Base, where you have to backtrack out of the area to get the Plasma beam, and any attempts to take the shortcuts resulted in more dead-ends. And the Plasma beam is in the middle of an area you've already been to. Prime 2 has a few instances of this, but it's not nearly as problematic.
I think the biggest difference is how long it takes to cross a given room. In Prime 2, rooms are designed in a way that allow you to cross them more quickly, with enemies being easier to ignore on repeated visits and fewer instances of long hallways or corridors. Prime 1 had a bunch of hallways in the desert level and avoiding enemies was much more annoying. These little things that make backtracking less enjoyable add up to make the experience less enjoyable for me.
Maybe I'm completely off-base about all of this and I've just gotten used to it by now. I sincerely found to level design in Prime 2 to be less monotonous and less frustrating to back track. And thinking back to the times I got annoyed or bored in the first Prime, I don't think the frustration would be alleviated with my increased familiarity with the engine or added motion controls from the trilogy collection.