If there is no reason to create sequels to X & Y, I wouldn't be surprised if Game Freak just jumped right into their next project. Just because a third version isn't as exciting doesn't mean that they have to make sequels. B & W had a huge sequel hook; it was obvious sequels were the best path to take. And the sequels turned out to be great, possibly even better than any game before it. But does that mean X & Y have to have sequels? Absolutely not! I'd rather they end the generation early than force out games that end up being sub-par because they want to start a tradition of creating sequels for each gen.
So would I rather have sequels or a third version? Neither. I'd rather have what works best with this gen. And it is way too soon to tell what that is. A third version that goes beyond what the previous ones have done, sequels, remakes in the form of sequels, a whole new gen...Whatever works best.