Nice to see you're still working on this. The new levels, bosses and the skills you get from them all feel pretty good. Noticed some new enemies in the old stages too. Some thoughts I had while playing:

• I think the archer enemy could use a bit of fine-tuning, like the wave the projectiles do could be slightly longer or something, it's really hard to judge where the safe spots are right now.
• The special weapon energy mechanic seems pretty irrelevant. I couldn't
  come up with a reason to use them without charging at any point in the game.
• Walljumps feel kind of bad, especially when jumping from one wall to another. The input buffer idea that someone else already described could be good.
• I managed to get some holy water vials stuck inside walls and not exploding when throwing them right next to a wall a couple of times.

Also, after reading some of the comments below I tried disabling vsync to uncap the framerate, and sure enough at around 1000FPS the bosses become almost completely incapable of jumping, so you definitely have some issues with deltas somewhere. https://files.catbox.moe/qwrs1t.webm

Here you go: 

• Audio needs some polish of course, especially the shoot sound. I feel like it should be more like a laser gun or a click. Also the sound for landing on the ground is kind of loud.
• I encountered one bug near the secret area in Fire Bot's level, but the rest was bug-free.
• Maybe the walljump pushes you a bit too far from the wall, but I can't decide.
• Also, I'm not sure if this is common practice, but you can look into creating an input buffer for walljumps — for example, if you press left (away from the wall) on frame 1, and then jump on frame 2, you can count that as wall jump. I know that fighting games do this, but not sure about Mega Man.

Overall, this is great. It's Mega Man, so you don't really have to change much from the base games. But it's a good clone with a qt operator.