One change I'd definitely like to see is to at least double the maximum number of Crash Bombers you can fire. In the original, you could only fire off 7 before completly depleting your entire stock. Compared to the Metal Blade which could be fired 56 times in total, it means you can never use Crash Bombers as an offensive weapon and must conserve your energy for that damn wall boss in Wily 3.
Anyone who has ever played through Megaman 2 knows what I'm talking about already, but just to restate, this boss is protected by Crash Bomber walls, and the sensors themselves can only be destroyed by the Crash Bomb. The bare minimum number of shots it takes to defeat the boss is 6 Crash Bombers, and that's getting both the two walls in the bottom right corner with one Crash Bomber in the middle of both. If you run out of ammo, you're screwed. You need to die, be sent back, and then farm enemies for more Crash Bomber ammo.
This sucks and is the kind of game mechanic that would be considered unexceptionable even in the 16-bit era, let alone today.
Ideally I'd like the ammo for the Crash Bomber to be increased to 21 shots, but even doubled to 14 would be a big improvement.
Speaking of weapons, another slight change that would make the experience better would be if the Flash Stopper could be disabled manually by pressing B. In the original, once engaged, you have to wait until it depletes all of its energy which limits its usefulness to only a few sections of the entire game. This alternation isn't as important as the need for a larger supply of Crash Bombers, but it still would be a nice improvement if you're going for an improved Megaman 2 experience in the first place.