Err... why would you ever need 12-16 .wads at once? Unload the unused ones, you don't need so many wads. It'll probably be the cause of your problem too, so why don't give it a try?
Heh, I only use 3 or 4 wads at a time, including the zhlt.wad... Oh, and -wadinclude will only include the used textures from that .wad file, so it shouldn't be a real big boost to the file-size.