Second, does it really make any difference how you gain your abilities storywise? What difference does it make if you beat a boss and then collect a power up or if you beat a boss and then your commanding officer says "oh ****, you're gonna need more weaponry"? It's the same effect either way.
It's the specifics that bug me. Receiving an item that grants you an ability creates a sense of accomplishment. Having someone grant you permission is like when you can't climb over a two foot fence because the game designers don't want you going over there. Nintendo has traditionally been very good at that sort of stuff. It's good game design to make the path you force the player to take, not feel like a forced path. A lot of people were turned off by the way Metroid Fusion unlocked areas at specific points. It wasn't enough for me but I guess this is. It just took more to step over the line for me than it did for Metroid Fusion haters.
Super Metroid is no different in that the reason you can't access this area or that is entirely the game being manipulated in that way. But it's done in a subtle way so you think less "I'm not allowed to go there yet" and more "I've tried to make that jump 10 times and I can never make it, I must need some item to jump higher."
Realistically it's dumbing down a game. It's no different than "hints" that in fact tell you outright where to go. You see a door that is locked because the game just hasn't unlocked it for you yet and you know not to bother. But with the Super Metroid design it isn't so obvious where you can or can't go so you try out different things until you come to the conclusion of which way to go. Locking away an area tells the player to not bother going in that direction. Same with items. You're on the look-out for new ones and in Super Metroid they were not always after a boss. It wasn't always obvious when a boss would show up or what items required you to fight one first.
Deep down we're looking at the same basic game design but the details seperate the difference between a game that holds your hand and one that doesn't.
Thinking about that, it would probably give Zelda a real punch in the arm to not tie new items so specifically with dungeons. If you're at a new dungeon you KNOW that some item you find there will be required to complete it. Maybe there's two items. Maybe there's none. Maybe this isn't even a dungeon.