ROTT's WADs only store sounds and graphics - game behavior is all intrinsic to the executable, so you'd need to grab the source code off the 3D Realms site and rebuild your own executable to make modifications to weapons and the like. As far as making new WADs are concerned, I
do know that Apogee gave the game support for loading replacement graphics in the style of doom. I believe you load them using the "-file" parameter when running the game from the command line?
Don't know how far along programs for
making ROTT WADs are, though. There's some old
WAD utilities for building new ones, but I've never tried them. There is also Birger's
ROTT Multitool which seems to serve the same purpose, but with a graphical interface.
For the record, I know that XWE can open and view graphics in DARKWAR.WAD as well, although I'm not sure if it is capable of saving new files into it or any fanmade archives.