To quote you, read up.
Company History|The Pokémon Company
In the core, yes, Nintendo has a majority..but it's joined with Game Freak and Creatures, which for the case of GF..has released games on non-Nintendo consoles (even though they are not as..releasing, in the amount of outer-Nintendo titles).
That said, to just..say things.
It should not, nor would it not, be a bad thing if Pokemon was the first IP for Super Nintendo World in the the terms of Orlando. Hell, it may even be a good possibility to..shall we say, set the direction of what they intend to do.
If Universal plans on making Nintendo and it's IP's Multi-Phased across the three parks, having Pokemon start off before Mario would be a big choice, that would bring still quite a bit of positive results. And especially if the fat plumber is the second-man for them; with having him head up Gate 4, it will be not as if they are putting in something that is..dated.