GameFreak is a small team (They were 80 people as of XY, but recent interviews state that both Black/White and XY required expansion) that's worked in 2D almost its entire history, thus you can't get a console Pokemon game from the actual Pokemon team- it's simply too much to ask. Then you run into the usual JRPG hurdle of the fact that building a detailed 3D world to current expectation is expensive, and Nintendo clearly lacks the confidence in Pokemon console games to get a developer qualified for the job; which they would have to do because the only teams within Nintendo with the resources for the job are the Mario and Zelda teams.
Genius Sonority's 3 games actually demonstrate the two ways to get around this and why neither is that great; Colosseum and XD have legitimate game worlds, but they're a fraction of the scale of the handheld games and are hardly the best looking anything on the Gamecube, while Battle Revolution looks great and has more effects, but you can't do anything with it, its just 12 backgrounds in which 493 pokemon and 6 different types of humans stand around and animate in place.
Confidence + outsourcing costs versus return (Which will be lower than the handheld games no matter what, basically) is probably your real answer in a sentence. Granted, this could change; Nintendo effectively created a new developer with Sakurai at the helm to deal with Super Smash Brothers (Granted, Sakurai's done non-Nintendo games, but its effectively the Smash Brothers house), but Smash Brothers is worth that investment.
And, of course, the fact that portable Pokemon games both make it impossible for Nintendo's portables to fail, and sell Nintendo portables to people who otherwise wouldn't buy them.