PokéBase - Pokémon Q&A
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Or some of them can't anymore?

If the transfer feature still allow Pokémon from those games to be transferred in present days. (If the system still work)

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I can hardly make sense of this question. What are you asking, exactly? If Pokemon from a gameboy advanced and (or?) nintendo ds can be migrated to the games on the 3ds? Please re-word this so that it can be better understood.
Yes, or if some of them can't anymore.

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Yes, I literally just did this 2 Days ago. Just note:

  • RBY/GSC cannot have Pokemon migrate up to the 3DS (as they can't transfer to RSE/FRLG) unless they are downloaded versions (from the Nintendo 3DS Eshop), then they can go directly to Pokemon Bank. :P

An example path would be: Ruby transfers to diamond via the Migrate option; From Diamond to White via Poké Transfer Lab, From White to Bank via Poké Transporter, and from Bank to Ultra Moon.

Hope I helped!

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Almost every Pokémon from Gen 3 onwards (with some very few fringe exceptions, like Spiky-Eared Pichu and Cosplay Pikachu, and I'm pretty sure Totems as well, since they can't be moved into Poke Bank) can be migrated/transferred to future generations via the Pal Park (Gen 3 -> Gen 4), Poke Transfer (Gen 4 -> Gen 5), or Poke Bank (Gen 5 -> Gen 6/7, and Gen 6 -> Gen 7). However, this is a one-way transfer; once sent to a future generation, it is impossible to transfer a Pokémon back.

For the fringe examples, the reason why they can't be transferred to newer games is because their data only exists in their debut games. The three examples I listed above are the only three cases I am aware of (if I missed anything, please correct me). The only other case of a Pokémon being unable to transfer is if it fails the Poke Bank's hack check, and even then, there are many reports of hacked Pokémon getting through.

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Beat me to it, but your answer is better than mine would have been anyway. Kudos.
I got sniped! Oh well, but you missed cosplay Pikachu as well :P

Edit: Much Is missed when I am tired. I see :P
No, I got that one. It's the second one I mentioned.