I'm on the 3rd level of Wily's Castle now, the dev team did an awesome job making sure you use every damn weapon as you go through each Wily level, and not just to surpass gaps, we're talking killing enemies and even minor enemies and subbosses having some noticeable effect against some weapons (like the Dragon losing it's flame body is you use Tornado Wind).
By the time I reach the end of a single Wily stage, my weapons are nearly depleted, and they don't recharge between Wily stages, I have to hunt for powerups (although admittedly, there's definitely some noticeable spots that are good for harvesting using the Gem Shield).
~HotShotX