Agreed on some of the light-dark world traversal but the more modular design should have made backtracking easier overall. Temple Grounds is the overall hub but as you progress through the game you can unlock shortcuts that connect the other regions directly. Seekers open up a path between Agon and Torvus, Power Bombs open up shortcuts from Sanctuary to the other two, and obv. Light Suit opens up direct teleports between all the main energy controllers. Prime 1's rough here by comparison - a point that was hammered home to me when I played the Remastered release and didn't get Space Jump first like I do every time I played the GCN release. You have to make *3* trips across half of Magmoor, across the exact same rooms, after clearing the Chozo Ruins. By the end of the game, some areas just don't connect directly at all too. There's an appeal to that kind of design too but the lengthy trips if you want to get anywhere can be a hassle.
Some of the design in Echoes could be cleaner though, yeah. The devs clearly wanted to play with the other world mechanic but the long loading times tended to make things more tedious. Maybe it would have been better if the transitions were faster but I don't think they had that luxury on the GCN hardware. Those games are built to keep only two rooms loaded at a time, and Retro already was cutting corners as is to keep the game running smoothly. Notice how two, large rooms are never directly adjacent to each other? On original hardware, you can crash Prime 1 relatively easily by Boost Balling too quickly through some of the connecting tunnels in the Chozo Ruins (interestingly, I don't think this ever happened to me in Phendrana).
A little surprised to hear you don't like some of the endgame bosses. I'll give you Emperor Ing as I've never been a fan of his flailing tentacle form that didn't like lock-on or his final form that always seemed to have some non-deliberate obstruction blocking his vulnerable spot, but most of the other endgame bosses are pretty cool. Spider Guardian and Power Bomb Guardian are fun puzzle fights, Quadraxis is commonly cited as a favorite among fans for its scope and grandeur, and Chykka... isn't quite late-game but it's my favorite fight in the game for how fast-paced and involved the second phase is.
I will freely admit I'm not nearly as in-depth with either Prime 1 or Prime 2 as you are I think. Just in terms of map knowledge and so on. I've beaten Prime 1 probably...four times total throughout the (many) years and I've only fully beaten Prime 2 once now.
I think my issue with Prime 2's backtracking is often the "feel" of it. That's an obtuse thing to say but as a player, the light/dark maps, the pretty damn long distances to get anywhere and so on especially truly tested my patience during the Sky Temple key hunt. I should add I played and beat this completely blind. I sat down with a pen and paper, old school style lol, and actually made lists as I was going. Same for the Sky Temple keys. I almost always knew what to do, just thought switching between light/dark on the map eight million times and going back and forth to portals every time...damn. I was really hoping they'd just introduce a portal item of sorts later on that just lets me switch worlds on the fly. The Sanctuary Fortress trek to the portals especially got on my nerves.
But again, I'll freely admit that Prime 1 may have similar issues but I think it didn't wear on me as much because it's less convoluted. Which again isn't always a bad thing. I do like quite a few aspects of Prime 2 going balls deep with the formula. The more I think about it, the more my issues might just boil down to the dark world stuff. There are some cool, clever elements with that though. I like how they'll have you solve a puzzle in the other world to create a pathway in light and so on.
Bosses. I think it DOES have a few pretty fun fights but personally, I find some of them a bit too convoluted and drawn out again. Like Chykka is a cool concept and I only died to it once but I just found the fight annoying overall. Bear with me I have to google these fucking names lol. Quadraxis was cool, you're right. Spider Guardian is straight up hate from me, thought that last "stage" of it was infuriating. But really my biggest boss gripe is the last boss combined with time limit Dark Samus. It's just another one of those "you could but...did ya have to?" moments that sometimes popped up in the game. Emperor Ing's mouth grille thing was confusing as hell, I really didn't know if I was playing it right or if there was a trick to it that I didn't get because shots would land maybe 30% of the time. Anyway...
And you know what, you are right, Magmoor in Prime 1 does get pretty annoying. That song is branded into my skull because I've run through it so many times.
Overall though, I still would give Prime 2 a 7/10
at the very lowest like I said. It's kind of weird because all the great things I have to say about it feel like a given because I expect everyone to know the Prime formula in general is fucking sick so I only really mentioned the negatives