Portability is a massive part of Pokémon. It's a massive part of why it's a success. It's a massive part of why it continues to be a success. If they remove it, they just destroy what it is to be Pokémon.
Portability is not the only reason why its successful otherwise every handheld game out there would be a success .. right ?
If you could catch pokemon like you do in Denpa men you might have a point but that's clearly not the case.
You seem to be ignoring my idea of making it multiplatform (WiiU/3DS) which solves both issues. As you mentioned before though the development cost would go up but if a large budget is good enough for Mario and Zelda games why not Pokemon ?
They can have all the features that are on Home Console on the 3DS in addition to the portability. There is no logical reason to bring it onto the home console.
Better graphics, better AI, better internet connectivity (ie always online whilst playing the game, unlike the broken connection you get with hand-held because of battery life), the other logical reason might be because fans may want it on home console.
Nintendo's handheld market share is rapidly decreasing due to mobile gaming if they want to keep their games relevant them cross platform seems as good an idea as any.