-looks at his 3ds- Eh... not enough buttons for the 3ds to be an effective N64 controller... While undoubtedly it could be done by moving some buttons to the touchscreen, it would be awkward as the least use buttons would be some of the C directions (A and B would have to be bound to Y and B as they are used most) which would be disorientating since two of them would be on the other side.... Unless you did ALL of the c-buttons on the touchscreen... but that would be bad for games that require the use of multiple c buttons simultaneously.
Of course, just from a pure hardware perspective we can't be sure if the 3DS even has enough oomph... but judging by the controls alone I'd say Nintendo would be very unlikely to persue that route.
As for pokemon pinball, I'd say it's VERY likely we'll get one or both of the games on the eshop eventually... It may even be one of the 10 games released via the ambassasor program... While a real pokemon game would be better, it would seem to be unlikely as nintendo can make a lot more money releasing them on the shop later. That and they'd have to release 2 actual pokemon games if you wanted to "collect them all" since you need matching sets... and I doubt nintendo would be willing to release 2 for the ambassador program.
So that puts pokemon pinball in the perfect spot as it is a pokemon game, they would only have to give away 1, and since it's not a true pokemon game they can save the real deals for the store later.