It's a hard call. For one, HAL is one of the best development departments in Nintendo. Their games are certainly memorable, and always amongst the best of the console. Examples such as the Stadiums (Even though I vastly prefer Colosseum/XD, it goes without question that they WERE some of the best games for the N64, which isn't saying much, but still...) and Smash Bros. talk by themselves.
However, I liked Genius Sonority in both of its games. I do believe they failed quite a bit in regards of the details, such as the Pokémon taunts when coming out and not using a hit animation when the attack is not very effective. Plus, they also left several things unexplained in Colosseum/XD. Still, they developed an awesome deviation from the now-boring handheld formula. Such a dark story, intriguing and various characters, a very bizarre world and the awesome scenarios were just astounding. Plus, they managed to outdo all handhelds, those that are now and those that'll come in one simple, yet important regard: they force you to use the Pokémon you get. Instead of catching and dumping in the box forever, you now have to use them at least for a while in order to purify them and complete the game. This endows the use of Pokémon like nothing else, and you get to know species that'd go ignored and used for Pokédex fodder in the carts. That's why XD was ruined with the incursion of the Purifying Chamber, killing the concept Colosseum had enforced so much...
Genius still needs practice, as their animations and vectoring still has sloppy mishaps (Use Thunderbolt in XD against Murkrow, and you'll see...), although they HAVE improved a lot since Colosseum. I'd say they'd be quite a good department to use in the design of this new game.
Still... why not both? HAL develops the fun factor and those juicy details, while Genius stands in charge of the animations and storyline, if any. I think that'd be ideal...
