I SUSPECT that Nintendo's tack with Pokemon is as a "clean up hitter" money maker franchise on already-established, heavily user-based platforms with a heavy emphasis on player<->player interaction. You don't have that same sort of interaction on consoles. Also, consoles probably have less of a reach into the younger demographics than handhelds, as well as a smaller userbase outright.
But in addition to that, console level production values also affects profit margins. It's worth noting that the Pokemon games come off as immensely graphically unambitious, which probably keeps dev costs down, and perhaps suits the limited size/ability of GameFreak, who co-own the Pokemon rights with Nintendo.
Pokemon is something of the pinnacle of Gunpei Yokoi's "innovation with withered technology" streak that Nintendo has in them. They found a fun, unique, and profitable formula that relies not on high-end technology but on the strength of a basic idea concept that works even on GB level technology. Throwing that on a console, without carefully re-examining what made it a profitable success in the first place, would be something that I consider as, frankly, short-sighted, careless, and ill-advised.
I'd love to see a mainline Pokemon experience on a console. Don't get me wrong. But I like the fact that Nintendo is being careful with how they handle the franchise and its unique strengths and position in their portfolio instead of buying into the "bigger is always better" hype that would lead to a quickie console release. I still hope to see a Pokemon Console Mainline RPG, but I hope it happens when it makes sense from Nintendo's point of view, and not just because my first instinct as a consumer when I get something nice is "make a sequel, but with twice as much EVERYTHING!"