The easy answer to this is "well, if you want to use those abilities, go back and do the side content/find all the expansions and such". But the vast majority of the time, all of your fancy-pants new abilities and weapons and such make going back through the game absolutely trivial and you almost certainly don't need those extra missiles and energy tanks to beat the final boss anyway.
I've been playing a few Metroidvanias lately - I finished Metroid Prime 1 not too long ago, I played through Zero Mission and Super Metroid, now I'm playing through Fusion and Timespinner, so this post will be Metroid-focused. This has kind of been on my mind lately, because it sucks to get an awesome late game thing but you only get to use it for one thing. You get Power Bombs in Metroid Zero Mission and the only thing you really have to use them for is to open the door to the final boss - there's some secrets behind power bomb walls and doors but not all that many.
But it's a weird conundrum. Part of the fun of a Metroidvania is getting new and exciting abilities to traverse the world with/kill enemies with/etc. If that dries up 3/4 of the way through the game, then one of the most appealing parts of the genre is gone. What are they going to do with that other 25%, anyway? If the nature of the game is unlocking abilities to gain access to new areas to unlock abilities to gain access to new areas, then once you've got all the abilities you should be able to just go finish the game, right? Unless you're blocked from finishing the game by some arbitrary lock of some sort. Castlevania: Dawn of Sorrow does this thing where you have to pass through three different doors with specific souls dropped by certain enemies. That's fine, but that's also just busywork if you haven't got those souls already (and it's busywork that really isn't going to take you a long time, so it doesn't add any meaningful content to the game).
A good solution to this might simply be secrets. And by that I don't mean "this hidden room with a health expansion in it". I mean, a secret area or something, with its own theme and enemies and a bonus boss to fight. And you have to access it by figuring out how to use some ability, or by gaining a new ability that isn't necessary for finishing the game - sort of a combination between Super Metroid teaching you how to wall jump in a hidden area and Super Metroid not requiring the Jumpball to finish the game, but with those abilities leading to actual new things and not just "cool shit you can do". But secret areas cost money and take time to make and I think most devs would rather put their money into something that people will actually see without going to GameFAQs.
I think this question becomes less relevant outside of Metroidvanias and RPGs though. It's a whole different ball of wax for RPGs - late-game "nuke everything in sight" type attacks would get real boring, real fast if they gave it to you at the 3/4 mark, so that kinda needs to be saved for the final dungeon and, perhaps, NG+.
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