I'm trying my best to break the game but even when I try to avoid the main path I go places where I need an item to continue, no choice. Plus it is beyond easy. The boss cutscenes are awful too.
The backtracking in super was just more fun. This game is just super straight forward puzzles and fights and I can just breeze through. I just speed through a room, carpet bomb for secrets, try to wall jump to places I'm not supposed to be, bomb jump up there, get stopped by item specific obstacle (wall jumping still is broken, you can't insta ball, no wall jump on single block). The backtracking in super was exploration. In ZM it tells you what to do and the areas are only interesting to traverse once.
I don't have reliable internet still, so I can't look up anything. Right now I have screw attack and am heading to tourian. Going to start a new save and try to intentionally avoid crucial items. Maybe it wouldn't be so hard if everything didn't funnel you into them.
Ok, certain things to note:
It's a remake of Metroid 1. They did in fact add more paths in order to make some sequence breaking possible, but you're dealing with the same general map.
The fights are pretty easy, I'll admit, but they weren't exactly tough in Super, either. I can't remember a single boss that was actually difficult to fight in Super, save for maybe Ridley. My advice to you is to just beat the game as you are right now, then on your next playthrough go through it again and this time try to do things differently. You know where all the items are, try to get to them in different ways.
The game telling you where to go isn't that big of a deal-it can be safely ignored entirely, you honestly never need to pay attention to that. The game only funnels you if you let it-and you sound like you've played Metroid games before, so you really don't need to let it. Claiming it's hard to avoid crucial items is a bit much, given that you actually do need the majority of them to get anywhere. It's a Metroid game, after all; getting those items are what open up your exploration.
Not gonna lie, a lot of your issues with this game sound like a combinations of "I liked Super better" and nitpicking. Zero Mission is a smaller game, but I think it's where the Metroid formula shone brightest. Super was just a bigger game.
Here's a few ideas:
Beat Ridley before Kraid
Go for low% runs. iirc, you can skip either bombs or screw attack, but not both.
Skip Ice Beam until just before Tourian.
Grab the Hi-Jump boots on your first trip into Norfair. Yeah, it's possible. You might need the Ice Beam for it though, not sure.
Get the Varia suit as early as possible. I think you can do it once you've got the bombs, but it's very tricky and difficult.
Just beat the game first before starting over. There's some extra stuff that you're missing.