Some opinions on the lvl 3 charge buster:
It's a straight downgrade for bosses. For what i managed to tell in 2 playthroughs, the regular charged shot does 3 damage, while the upgrade does 2 damage per tick. It makes sense, is to balance out the continuous damage, however, it seems to take a little while until the initial tick and a lot more time until the second one. This is a Mega Man X game, there's barely any instances where you can consistently get the two ticks of damage on these high movement bosses. With Snapper is easier because he doesn't jump around and even then, but most of the time you have to time it perfectly right when a boss is right about to start an attack that makes them stand still in place for a while in order to pull it off, but if you shoot a little early or late either the beam's active time finishes early or the boss moves away or gets into an invulnerable state. Even then, there's bosses that will just never get the 2 ticks of damage like Ride Armor Vile or Fortress 1 (to my knowledge).
My proposal is this: The beam does damage right away and on its first tick it does the same 3 damage as the regular charged shot. Then I got two additional options: 1. The beam ignores the bosses' recovery invulnerability and deals 1 0.5-1 damage each subsequent tick; or 2. The bosses' recovery invulnerability gets reduced a little for the buster beam and the subsequent tick does 2 1.5-2 damage, so you get that second tick more reliably on most bosses and, in those that you don't, at least you did the regular 3 damage.
Currently, what my mind is most busy with during boss fights is with timing the charge so i shoot the lvl2 instead of the lvl3 shot, rather than the bosses's attacks themselves.
Edit: Looks like the time the beam takes to start doing damage to some enemies might be a bug
Edit 2: changed the suggested damages