This is a fascinating and fun idea for playing the game. I'd thought to myself that a Dark run in Ruby / Sapphire / Emerald would be a great idea, and this thread proves it. Ghost one might be interesting, too, but you'd be limited to the only six guys available, really, and Sidney & Phoebe in the Elite 4 might be a bit of a challenge.
I'm more interested in doing it for fun, and not necessarily for the "challenge." It's fun to think of your character winning the Elite 4 and setting up a typed gym with your team. I'm not so opposed to trading in some guys to start out the game with - did this for my Platinum run-through and it was really a lot of fun to mix & match non-legendaries to come up with an interesting team of guys that I wouldn't normally use, just to see how the team would mesh together. You'd pretty much have to "trade-in" to get teams of certain types, just because there are so few guys - a dragon team for Ruby doesn't have too many options; an all-electric team on any of the Gen III games - or even Gen IV - is a little sparse in the options. One of the redeeming features of Gen V is that they're really rounding out the dual-type matchups for fun run-throughs like this. Stuff like Ghost-Fire, Dark-Dragon, Dark-Fight, Bug-Electric...they might not all be competitive, but they are certainly interesting.
The original RBY is more boring, IMO, just because the options are so limited for a themed team like this. Fire, Rock, Grass, Electric are just some that are BORING, and Steel and Dark are right out altogether. Fire is still boring in HGSS, Electric has more guys but no more variety (not until Gen IV that Rotom makes it interesting)...hmm.
I like the idea of a Dark-through of Hoenn; need to do a run-through of LeafGreen sometime (have a SpaceCenter Deoxys and a 10ANIV Celebi on the cart that you can't trade out until you have the nat'l dex)...maybe I'll do a themed set with that, but it's just SO limited. I really wish that the FR/LG remakes let you take through anybody, even from the national dex. It would completely break the balance, but it would be fun to go through the game like that - a Normal run-through, perhaps, with interesting guys like Kecleon and Castform, a Fight-through with Breloom or Blaziken, a Ground-through with Claydol and Flygon. Lots of possibilities for fun. You'd figure that, if they're "making" you go through the games again, the least they could do is make it wide open for fun like this instead of restricting you to that game's dex, or at least making it optional.