1. Stage length - how to people feel about this? I always felt many of the stages in MM1-6 were a bit too short. In MM9-10 they were a bit longer, and in MM Unlimited, even more so. In my hack, level length falls between that of MM9-10 and that of Unlimited. Is that fine to most people, or is it too long?
2. Robot master weapons - is it fine that they don't work on absolutely every enemy (such as Metal Blade not working on the Sniper Joe walking machine in MM2), or is this something people perceive as annoying? In my hack, a few rooms would in my opinion be too easy if f.ex. Rain Flush worked on the enemies there, but maybe that's an option you should have in order to pass specific challenges you don't like?
It all depends on the weapon and enemy of course, but in a case like Rain Flush, then yeah it is important that it works on most things. That is the point of the weapon, with heavy energy use as a drawback. In fact, it's pretty much the point of the entire classic MM gameplay: you CAN use weapons to help you, some will work perfectly in some situations, weaknesses for every enemy and bosses, etc and it's up to the player to find out when to use which weapon, to balance his weapon use, or to decide if he wants to use the weapons at all, basically the player decides how much challenge he wants. If Rain Flush doesn't work in situations where it's needed the most, and where it makes sense to use it, than that sucks and it renders the weapon almost pointless, and if you ask me it goes against the "Mega Man logic".
Plus, if there is nothing, no visual, for the player to guess that Rain Flush might not work in that particular situation, it will come off as unfair or glitchy, and then every time he'll want to use Rain Flush he'll wonder if it works.
Of course, if there is a visual cue of some kind it should be fine; like let's say Rain Flush doesn't work on enemies with umbrellas (or who are umbrellas).
This makes me think of Gravity Hold in MM5. Gravity Hold, like other things, doesn't work on shielded enemies, or enemies which are in "shield state". However, there is no visual cue, or even a sound, to tell it doesn't work. I've seen many players get confused by that, some even thinking the weapon doesn't work at all on some enemies and on bosses, and I'm talking players who know the game very well.
Good job with his hack, it looks really good. The only thing I don't like the underwater screenshot, something about the colours don't fit right to me. If it was me, I'd go with a more yellow-ish sand, light blue water, and make the spikes grey like the rock.
Edit : btw I see you're mentionning glitch fixes and lag reduction. Are you aware of thise guy's hacks ? http://www.geocities.jp/borokobo/neo/download.html
There is an "optimization" patch that gets rid of any lag. There are two versions of it, one which adds other things as well like switching weapons with select.
He also has a hack that allows jumping during a slide when underwater.
These are for Rockman 4 and not Mega Man 4 but I'm sure you'll be able to connect the dots.
Also one thing I'd like to see fixed is the glitch that allows you to remain fully charged for a charge shot even after switching weapons as long as you're holding B when getting back to the buster. If MM4 works anything like MM5 (and I do know for a fact that they are close) I'm sure it's just a matter of setting the charge counter to 0 when switching weapon and/or opening the menu.