Sure, sounds simple. Now all you have to do is put together a team, create new models, write new code, play-test and rebalance the game, design new maps (because you are sorely mistaken to think that maps specifically created for two-faction games will be useful for three-faction games - how can you make all three bases equidistant without completely moving the existing bases?), come up with some third type of combat besides ranged and melee to make the third faction truly distinct, then put up a website to host the download and aid in troubleshooting, host a server for play-balancing and promotion, get moderators for your forums and admins for your server, and voila, no problem, a new three-faction mod.
Get back to us when you have come up with the new replacement for weapons/classes, have envisioned this Mythical Third Race and its various buildables and other artifacts, and have gotten three 2d artists, two 3d modelers, three coders and two admin/mod/beta-testers on-board.
"Oh, it's so easy!"
"Someone else please make this now that I've said how easy it is."
lol