My friend and I's explaination for most of Samus's starting over in powerups anytime it's not explicitly stated is that she sells all the weapon upgrades for booze money xDRandV80 said:As much as I love Metroid, making sequels suffers from a state I call original flavour works best. The pattern that NES Metroid, SNES Super Metroid, and Gamecube Metroid Prime all followed: start on bird people planet with the pea shooter, proceed through various themed zones finding power ups on the way. While Metroid Prime actually did this it gets a little contrived if you make her somehow lose her powers at the start of each game through some excuse to put Samus in the 'proper' starting state.
In all honesty though, that never bothered me that much since provided a reasonable explaination while allowing the metroidvania style gameplay to continue. They could have a game where Samus Starts out fully powered and slowly loses powerups, making it more difficult to proceed. That could be done interestingly I think.