>main character gets an awesome ability from an upgrade
>gets to keep it in all of the sequels
>But somehow loses a majority of it or flat-out not allowed to use it at all, because game reasons.
Bullshit, you dont get to keep the enemy armors. If by keeping the new abilities you mean keeping improvements on gameplay, then pretty much every platforming game does. Mario keeps the upgrade of "getting attached to walls" and to triple jump
It wouldn't, she would be way too overpowered. Plasma Beam, Power Bombs, Gravity Suit, Super Missiles, Phazon Utilities, Space Jump, SCREW ATTACK
The only way I could see her keeping abilities is if there was an immediate sequel to Metroid NES (but before Metroid II). The most powerful weapon she could have is the Plasma Beam, BUT in Metroid NES, you could only hold one weapon, so the next game could be her having the Ice Beam (because it is more useful for Tourian).
If any other game does this with the full extent of her arsenal (MP1->MP2 or Super->Fusion) it would have to be the same scenario in the beginning: Start off with awesome gear, but get sideshotted by something, causing her to lose those awesome stuff.
Im assuming you're talking about how it would work after Pime
I dont see it working if we're talking about keeping the upgrades throughout the entire game.
We'll assume that Phazon won't come into play in the next game, so Phazon Suit and Beam are useless.
She has immediate access to Wave Beam and Wavebuster, so she can stun and paralyze almost any enemy in the game.
She has immediate access to Ice Beam and Ice Spreader, so she can freeze just about any enemy in the game and make Metroids a complete joke, unless they introduce non-freezable metroids.
She has immediate access to Plasma Beam and Flamethrower, so she can melt and incinerate enemies if she so chose to.
She has access to Power Bomb, so she could clear rooms just with a press of a button.
She has super missiles, which has always been fucking powerful in all games.
Unless every enemy had a gimmick or a resistance, she would never have a hard time