It would be a watered down spin-off so that it doesn't eat into the main series sales, this is exactly what happen with the Colosseum and XD games.
The truth is the spin off are filler to tide people over until the next game in the main series get released.
Let's use our imagination for a second. Take the Pokemon mainline games, everything about them. Now, put that in a fully realized 3D space ala Ni no Kuni. Then you could possibly even add hunting elements such as seeing bird tracks in sand or claw marks on a tree. Even if it's functionally the same, imagine it bigger with a lot more details. It isn't watered down.
Why would you put an option for real time battle in a main series Pokémon game? It works fine in turn base.
It works fine as a turn based game. Another poster and I was discussing how the game could be made to feel more like the anime. Along with more, shall we say immersive gameplay elements outside of battle, adding a real time element to wild battles would make it feel closer to the anime. Trainer battles are supposed to be more structured, hence the turn based system. Having that system be real time, but with an ATB or similar system would give the battles a more frantic pace. Since you are still choosing between four moves per Pokemon it wouldn't get too complex.
Pokémon potential isn't being wasted at all by not being on the home console.
I'm not saying that, not quite. In general I think the Pokemon franchise has wasted potential because the mainline series of games hasn't really changed since generation 1. Sure there are a few more Pokemon types, new battles types and other things; but essentially it feels exactly like the original. And that's fine, the games are still fun and they are still extremely popular. All I'm saying is, at the very least, imagine that formula except with a compelling story and interesting characters. That alone would elevate the series. Then imagine all the things they could do creatively if they had much more power and freedom to work with.
It's not that Pokemon is bad - it isn't - it's that it could be so much more, especially since so many people have strong nostalgic feelings for the franchise. What I'm talking about aren't ideas I think Nintendo should necessarily employ, I'm just speaking from a "Wouldn't this be really cool." point of view.