Just finished Prime 2: Echoes for the first time and yeah I think it's the weakest of the three so far.
Really didn't like the last two fights which were just a slog. Plus with Prime when you scanned a boss it would show you critical information on the pop-up. Prime 2 will give you "some" information, but then you have to actually go into the menu and read the "full" entry to get critical information on how to beat it because you're expected to do something that you've never had to do at all during the game.
The menu's wouldn't be so bad if they were the same as Prime, but the "rotating" choices and number of them make going into it too time consuming as well.
The automatic damage in Dark Aether is a nice idea, but I'd find myself just standing in the light bubbles waiting for health to recharge. It's arguably too late in the game before you get the Light Suit, but I can see how getting it any earlier would negate the point of the light bubbles.
Enemies are far too spongey (Especially early on) and the world is a lot more of a chore to navigate.
All that said it's still a great game, just maybe a touch too grating at times.
Corruption up next which I remember enjoying so we'll see how it goes.
Oh and Prime 1 is a masterpiece and is easily up there with Mario and Zelda for 2D-3D transitions. Both of them feel different from their 2D counterparts and while Prime isn't quite as good as either Mario 64 or Ocarina of Time, it's easily as impressive as a work of translating the game design to 3D. The backtracking for me isn't particularly bad because everytime I went somewhere to do something, I was getting other stuff on the way as well. 3D in first person was always going to result in a slower, more considered game and the pay-off in terms of a more immersive world was worth the reduction in movement speed and agility and I never once felt like I was hamstrung by it.
You could also argue that there are "lore" reasons why you can't use the ship in Prime. It's mostly set underground and the only real "outdoor" area apart from Tallon Overworld (Where the ship is), is Phendrana, where the Space Pirate base is set up. It's not inconceivable that they have Anti-Air defences. But I admit that's a stretch.
In Echoes your ship just gets damaged at the start.