Pokemon games for home consoles are either shallow ones or simply not as good as the main series titles.

It's a Massively Multiplayer Offline game.

Well thats simple
pokemon is well suited for the portable consoles. You could bring your game to school and trade with your friends. You could meet someone who has a mudkip and trade with them right when you see them. You cant bring a home console every were you go.

to sell their handheld, they have enough big series on consoles already

Pokemon wouldn't do very well on a home console

Pokemon is partially the baby of Gamefreak and the idea of making a RPG on the limited portable system. Over time as the portables have increased power, they have been drawn forward but at the time of its release much like Dragon Quest before the Square Enix merger, they've kept it simple and true to the core concept that got them the fans they have had today.

In doing so, it probably has taken the teams a while to get used to the new technology although thanks to the Pokemon generation cycle they are probably in good position in time for Pokemon X and Y.

But the fact is more so with the current generation, portables are the gods of Japanese gaming, console gaming isn't where the focus would go to especially after the last few attempts.

Think of it this way. One family may only have one Wii, while the same family may have 4 or 5 DS units depending on how many people are in the family. If they make a Pokemon game for wii it has the potential to sell one copy to the family, but 4 or 5 copies for DS. Everyone experiences their own adventure on the portables, can trade with each other, can take it wherever they want, and so on. It is more personal and it is what Nintendo will always do.

It's hard to give the OP anymore answers because everyone has already reiterated what other people have said. Now we just sound like a broken record.

pokemon mmo done right would destroy anything else on the market

Pokemon is a very grindy experience, and it's pretty low key. It's not like there are tons of big flashy moments that demand a big screen. It's not especially flashy from a graphics standpoint (creating 650 HD models might be a bit much). I've never really wanted to play Pokemon on a big screen or anything. It's perfect for trips, commute, or casually playing while I do something else, but I don't fee like taking up my TV with EV grinding. The online features could really be implemented on a 3DS anyway, so I just don't see the benefit of console games for the franchise.