The fact that it could potentially come out around the same time as the 3DS makes it interesting. Game Freak are pretty good at milking their engines for all they're worth (How many millions of games have they sold using the Diamond Pearl engine?) Would they be able to drag another DS engine out across the third game and Ruby/Sapphire remakes given that the 3DS could be a GC-level machine?
Every new generation, so far, has had a new engine that is then used across the entire series. Red/Blue/Yellow ran on the same thing, as did Gold/Silver/Crystal etc... If it's a true reboot, then I would hope they'd start fresh with a new engine instead of trying to hack the old one.
The interesting thing here is that you'd expect the sequel to Black & White to be on the 3DS, so are they planning for the 5th gen to be fairly short or do they plan to carry it across consoles? If the story of Game Freak being one of the first places to get 3DS Dev Kits is true then it could be that Nintendo are trying to make the game work on both.
Thinking about it, I don't think Game Freak would be too concerned if their Pokemon games look a little behind the times.
I still reckon that one of the new games will be a DS game and the other will be a 3DS game...