For the most part I think the musical arrangements are fine, but I can't help but feel that the backing part of Buster Rod G's theme is just always kinda stuck chasing after the melody. It sounds fine instrument-wise, but placewise on the module it seems off. Consider moving a couple of notes in the backing so that they play earlier and as a result sound better when used with the melody.
The timing is accurate to the original song. The background chords in the original song are somewhat syncopated. I don't feel the need to change this.
I was kinda disappointed that Wily Tower 3 was used in BRG's theme, but none of the others! In hindsight I understand why - neither of the other two showed up in the actual Wily Tower at all, and BRG only showed up on the third stage - but when the first cover was released I imagined you guys were gonna incorporate sections from other tower stage songs (Tower 2 and Tower 4, I'd imagine, since Tower 1 is kinda weird) intro the other two. Probably just a personal gripe though so if you don't feel any need to change it then go right on ahead.
Yeah, that is exactly why it was used in BRG's theme. To make up for that in the other themes, we decided to mix them slightly (especially HSH's theme), but I won't go as far as incorporating one of the other Wily tower themes. (BRG/Wily 3 happened to work well as the songs were already in relative keys, so I didn't have to transpose the melody)
I think you said somewhere that each playable character would be fighting one exclusively? Is it too early to give away that distribution, or could we have an explanation in advance?
Mega Man fights Buster Rod G.
Proto Man fights Mega Water S.
Bass fights Hyper Storm H.
*very long post which will inflate my post size*
I'll come out and admit that the sprites were somewhat rushed in order to upload the songs (not a conspiracy

) but they are being polished. We ourselves have noticed the issues with MWS and the spriters are working to correct them. To add a note, the "shine" on BRG's head is actually a part of his design
here.
As for color limits... we aren't strictly adhering to color limits
if we think that having an extra color would be beneficial to the sprite. It is likely that MWS will lose a color but HSH probably won't due to his size. And on that note, our HSH sprite is actually
smaller than the Wily Wars sprite (by 4 pixels). The battle is just a matter of good game design. It will be doable.
Also, it should always be assumed that feedback is welcome, even if it is not explicitly stated.