With the inclusion of 3V3 battles in Black and White, an RTS game isn't far off, right?
 
I mean, that crazy-ass rock-paper-scissors-ice-electric-whatever-else in an RTS setting would be really fun. 
 
And I would suck at it, like all other RTS games.

" I mean, that crazy-ass rock-paper-scissors-ice-electric-whatever-else in an RTS setting would be really fun. "

The idea has great potential, all the elements act like a perfect system. 

I've thought of this before. It sounds like something that could be really fun. Of course you would have to throw out the limit of 6 pokemon, but then again a 6v6 RTS could work. 
 
Nintendo seems pretty adamant about not changing the basic formula of the game, but this could at least bring a nice refreshing change to the franchise.
 
Oh well, yet another pokemon game that would be awesome to have, but like the MMO will probably not happen.
 
We can always hope though!

RTS's are already completely Rock-Paper-Scissors, so no change there.  But there's zero lore for this.  And Mewtwo would beat everyone.

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" @FinalDasa: But it's not Pokémon.  Do you actually envision a horde of pikachu going to invade your enemy's base or something? "

Maybe a Strategy RPG, like Tactics, but I don't see how you could make a full on RTS, especially Nintendo.

Pokemon's system is iconic not only because of its simpliciity to get into, but also because of its hidden onion-like layers of depth. Trying to radically change this would not only alienate the Pokemon fan base (and let's be honest, there's a lot of kids amongst that crowd) but it would also throw out all of the subtle complexity which makes the series what it is today. 
  
Subtle innovation is a good thing that keeps the system fresh and provides incentive to play the new game rather than keep the old ones. I don't even really play Pokemon, but I would have to say that its battle system is one of the best in the RPG world due to the fact that the core of it has remained unchanged for all these years, and the reason its remained like that is because people like it. I don't think a radical revolutionary revamp of the core gameplay is what either Nintendo or fans want or expect out of a new Pokemon game.

" @FinalDasa: Yeah, they'd probably figure something out if they actually wanted to make an RTS.  But I really don't think that it would please both adults who grew up with the franchise and kids entering it.  Pokémon games have a slow start and are quite simple to comprehend, which is appealing to kids.  If they made an RTS that was too complex, kids could possibly get frustrated with it and if it was too simple, older people would have no fun playing it. "