Fusion was terrible.
That game was flawless! I've only ever seen three criticisms of that game, and I don't think any of them hold any water.
*It has a progressive plot. Metroid games aren't supposed to have a progressive plot.
*There's dialogue in the game. Metroid isn't supposed to have dialogue.
*It's linear, I can't roam the entire ship freely until the last part of the game.
While you can argue that those changes lose the open feel and sense of loneliness that other Metroid games have, they were implemented brilliantly and parts of the game retained the exploration and isolation that the other games had. Sure, some areas were sealed until later in the game, restricting your movement, but a lot of the rooms and areas were gigantic and when you went in to explore those areas, you still felt very, very alone.
The SA-X was superbly executed too. That thing was terrifying and helped to create far more atmosphere than anything in the other 2D Metroid games. On the first playthrough, I spent virtually the entire game scared that the SA-X might show up in the next area. I nearly smashed my gameboy when that damn computer told me to go into an area that SA-X was actively exploring.
Instead of focusing on the parts that changed, focus on the good bits.
*Superb detailed, brightly coloured 2D graphics.
*A highly regarded understated score used to fantastic effect throughout the game.
*An engaging, perfectly paced plot.
*Tight, responsive controls.
*The SA-X.
I think the only valid criticism of the game is that it's far too short.
