Most of my problems with Fusion are more the presentation of everything. Super Metroid does hold your hand but it is mainly early on by trapping you down in the lower Brinstar/Norfair until you have Ice Beam/Varia Suit/Speed Boots but after that you are free to leave and you are left with a world to go off and explore until you get to the lower Norfair near the end. There is still a standard path and as long as you find everything along the way it becomes clearly laid out, or else you get to run around aimlessly and use the map to find everything.
Fusion holds your hand the entire game in an entirely explicit way. Instead of guiding the user through the level design, they throw story at you, open up a door and tell you where to go and what to do and why. When you are done, come back and listen to us tell you where to go, what to blah blah blah. All of the story and explanation as to why the game will not let you go through x door is only slowing down the progression and pace of the game. Later on your way back gets blocked but there is still really only 1 way to go. I feel all of this is the antithesis of what a MetroidVania game should be like. Let me choose where to go and how to screw it up.
I also hate how the run has worked in pretty much every game post super metroid. Super Metroid had a nice ramp up in speed. Every other game now has 3 speeds. Move, Run and Super Run(After x distance) with no build up between any of these. To my recollection Fusion introduced this and I stupidly hate it. It is just pointlessly slowing me down :/