All this talk of Metroid: Fusion is starting to convince me to snag a copy of it. I loved Zero Mission, but what few minutes of Fusion I played in an EB way back when turned me off. I guess I should have given it a chance. It sounds more awesome than I realized.
I haven't minded the RE4 sections as much, but they really, really needed to make Samus walk more quickly in that section at the end of Sector 1. That was infuriating...even Leon got a run button.
In general, the story conceit of Adam authorizing Samus' abilities doesn't bother me all that much, but it is silly. IMHO, it would have made much more sense to make it so that something on the Bottle Ship was suppressing Samus' abilities; given that the GF scientists examined her suit during the cloning process, it would make sense for them to have learned how it would work. Since Samus was ostensibly the only person capable of stopping the Metroid/Space Pirate threat originally, it would also make sense that they would want to prevent her from finding out what they were doing on board the ship. Adam, or someone else on the GF team, could have been working to override the bottle ship's suppression during the course of the game to unlock Samus' abilities more gradually. Perhaps that's just as ridiculous of an idea, but perhaps it would have been more palatable to long-time Metroid fans.