I've played a bit of the wad and this is what I've got to say:
The 3do weapons for Hargrove are out of resolution so they look kinda small and I think you should go with the PC weapons only since you don't have 3do versions of all the weapons.
I agree with the other people with the doom 64 weapons in that they should be different.
The shot gun could fire faster but require a short reload every 6 shots (I would go with a short goldeneye style reload). The BFG could act as a heavy rocket launcher, have the projectile go slow but do a lot of damage and have a large explosion. The rocket launcher that seeks is fine, leave it as it is. The plasma gun could be less accurate but do more damage. The chain gun could be more accurate but have a longer speed up time or fire more hitscans to stun enemies. The pistol could do more damage but require a reload. The super shotgun could shoot two shots in quick sequence instead of both barrels at once.
Make the music a seperate addon so it doesn't raise the file size too much. The shadows on the monsters are a bit too dark so maybe make them more transparent.
You could make the duke nukem raygun thing be more unique by making it turn enemies to your side or something.
I remember you saying something about removing the wolfenstein class but I think it would be a good idea to combine it with the Rise of the Triad class. You could have the mp40 instead of the dual pistols and have the chaingun instead of the mp40. Just use the chaingun sprites from the mac/jaguar version of the game,
Overall, this is a pretty nice mod so far and I agree with Sgt. Mark when he says the weapons feel very powerful.
