Simple enough question. Which, on a whole, do you prefer?
While I'd say the main series is more satisfying to play and has considerably more elements (team building, competitive battling, Pokédex completion, etc.) it's honestly starting to wear out on me. I'm not big on most of the hardcore stuff anyway. Of course I'll buy whatever they come out with, but I can't help but wish for more innovation and freedom.
In recent years, meanwhile, the spin-off games have increased in quality and multitude. If this were only a few years ago, this wouldn't even be a question, but now it most certainly is. At least to me. I'm a bit concerned we're going to get stuck in a Mystery Dungeon/Ranger rut and the concepts will grow old, but hopefully they'll continue to branch out and establish new, unique directions for the franchise. I'm kinda hoping to see less RPGs (and puzzle and pinball games) and more new genres. Like maybe a fighter game, which would be perfect.
Kinda sense main series will win by a large margin, though, heh.