I doubt if 3DS tech is up to this task, but I think it would be cool if you actually had to scan around you (using the built in cameras) and pokemon would appear in the video, dodging around and you have to get them Pokemon Snap! style in order to catch them, as an option within the game (kind of how the PokeWalker is an extension into the real world from Pokemon Heartgold). Maybe those coins you earn by walking with the 3DS could give you opportunity to take a certain number of shots a day, and offer some exclusive pokemon.

Of course, without AR cards I don't think this would work, as how would the system or game determine distance or surroundings?

It would be nifty if maybe the AR cards could be used for some kind of geocaching scheme. Imagine you are walking through a national park and your 3DS beeps, because someone with (3DS Pokemon game with a built in GPS) marked a hidden card nearby for you to find, maybe under a rock or something. You uncover and scan the card and a wild pokemon appears. Maybe the time it's been hidden there gives value to the pokemon you are able to encounter, like a higher level or rare hold item..

Of course, then Nintendo would get flak for encouraging littering so..

I guess just ignore everything I've typed, it's all pointless.