Oh, so instead of losing her powers, she now needs to find reasons that show an absolute need for her powers and send in an application to military bureaucracy to use them.
Well, I suppose that would explain why you get a new power directly after a boss battle.
I picture a conversation like this happening:
"FUCK! If you'd just let me use my super-missiles, I could've beaten that guy without nearly dying! If you continue this habit of nearly killing me, I'm going to murder you when I'm done with this."
"Erm... Okay, you can use your super-missiles.... Just only 5 of them at a time though, okay"
"...Are you going to let me have more if I need them?"
"No. That's the maximum, we don't want you destroying the place. Got that?"
"..." *sound of Samus turning back to her ship*
"...Okay fine! But could you at least find us some souvenirs or something? Just consider it a trade."
*Shoots a random wall, picks up a shiny rock*
"Here ya go, 5 more super-missiles."