You might never actually catch 'em all.
http://www.nintendoworldreport.com/blog/27251
My Pokédex 3D stopped downloading Pokemon the other day. This was a complete surprise, since I'd scanned every AR Marker available on the Internet back when the app first came out, and I was getting three Pokémon a day: two in the morning, one after work. It ran like clockwork, until yesterday. Yesterday, my 3DS got no Pokémon, despite missing four of the elemental monkeys and several different forms of existing Pokémon, like Deering or Sawbuck. Some internet research turned up some annoying findings: without other people who also have Pokédex 3D, I'll never have a complete Unova Pokédex.
Turns out, there are certain Pokémon you can only have one form of, or one kind of, and the rest you have to get by trading with friends (with the "Give/Receive" function in the menu). Here's a list of Pokémon that you'll only get one form of:
Deering, Sawbuck, Frillish, Jellicent, and Unfezant
That leaves three versions of Deering and Sawbuck, and one version each of the other three for you to get by trading. Furthermore, you'll only get one of the elemental monkeys and its evolution. I got Pansear and Simisear, but if I want Pansage, Panpour, Simisear, and Simipour, I'm gonna have to go do some beggin'. Finally, and this is the best part, you'll never get six Pokemon through SpotPass--you have to get them by scanning AR markers: Victini, Cobalion, Terrakion, Virizian, Reshiram, and Zekrom. It's not difficult to find an AR Marker website, so don't fret, but it's still a raw deal.
I understand this is Nintendo's way of adding typical Nintendo trading functionality to this useless app, but in North America, especially ALASKA, it's just not gonna happen. I can only hope these missing forms are downloadable via SpotPass in the future, because I hate to see missing Pokémon in my 3D Pokédex.