So I went through and compiled a list of all the gen 1-3 Pokemon who had less than 10 cards printed in at least one of the Pokemon in their line. I think for this set we're making, we should try and include as many of these as we can. How many have been printed is written next to each Pokemon (according to Bulbapedia).
http://pastebin.com/evxSaN4ZSome Pokemon I think we should definitely include no matter what:
Abra/Kadabra/Alakazam - I think we all know why this one has so few cards.
Tyrogue/Hitmonlee/Hitmontop/Hitmonchan? - Not only because there's so few Tyrogue, Hitmonlee and Hitmontop, but because it could have an interesting dynamic where each evolution has a completely different use in battle. This also made me think that maybe we should make Baby Pokemon into just Basic types and have Hitmonlee etc be Stage 1 cards.
Krabby/Kingler - Least cards out of all gen 1 Pokemon.
Chikorita/Bayleef/Meganium - Starter line with the fewest cards.
Sudowoodo - Few cards on it's own, but Bonsley only has 1 card ever released outside of Japan.
Snubbull/Granbull - Has few cards, but it would also be nice to have as a Fairy type since I believe it's also the fairy card with the fewest prints.
Regirock/Regice/Registeel - Legendaries with the fewest prints in relation to their age.