First off, I'd like to compliment all the hard work that's been done on the mod, and congratulate the team on a successful beta release.
I've not had a tremendous amount of time to spend with the first beta, and none at all with the recent patch, but there are two things right off the bat that I think could be improved, or at least discussed.
The first is the matter of the body armor. In the original, a clever tactic was to find armor for yourself, and then destroy others you came across to give yourself an edge. After a few minutes and several clips spent on a vest, it remained undamaged. If this has been changed since the first beta, then disregard this point.
The second matter is the music. As excellent as the remixes are, I can't help but think that the option of toggling the original soundtrack would be...just fantastic. I can't even think of words for it. The soundtrack has been ripped several times, and at least once in high quality, directly from the game ROM itself, so the files shouldn't be difficult to come by.
As per the legality of that last suggestion...I can't speak for it, though I would imagine it wouldn't be crossing any boundaries you haven't already and gotten away with.