This is the problem I tend to have with Pokemon. Im always chasing that original great memory of playing Pokemon Blue when it first came out but no Pokemon game since has really managed to keep my interest. The games are just way too similar that if I dont have the hook of wanting to get the next load of new Pokemon (which just seem to have lazier and lazier names/designs) then it doesnt feel like there is a point in playing.
I would love to be able to play a massive home console RPG for Pokemon. As many people have said many times, Ni No Kuni would be the perfect game to look to for inspiration.