I don't think Nintendo will ever give up the handheld market if they maintain anywhere near 3DS sales. they have been making a lot of money with the 3DS, if not for the Wii U's failures their numbers would be a lot better.
they do quite well with BOTH software and hardware in terms of profiting.
However I do have to disagree with you to some degree. Pokemon is definitely one of Nintendo's biggest franchises, but I think its fairly safe to say if Nintendo released a very simple Mario or Donkey Kong game that they would likely do excellent on mobile. A lot of casuals at some point in their lives have played a platformer like Mario and for a few bucks would pick it up for their phones
I mean look at some of the stuff people play on mobile, things as simple as slicing fruit that flies at you have gotten incredibly popular. no doubt a release of like Mario Bros 1 on mobile would do incredibly well
I'm with your overall sentiment though, Nintendo is unlikely to have anywhere near the market on mobile overall as they have on their own handheld platform where they are less restricted.
Its true Pokemon is to some degree an exception, like you can't walk into any kids or teenage trendy store without seeing Pikachu tshirts or Pokemon cards and things, even to this day
