There are currently 3 "paywalled" Pokemon, meaning you need to spend money in the game to obtain them.
1. Mewtwo - can only be obtained by first reaching VIP 12 in game, then you will be able to purchase this bundle for 4,880. There are currently no other ways to obtain Mewtwo.
2. Blaziken - can only be obtained by first reaching VIP 7 in game, then you will be able to purchase this bundle for 1,280. There are currently no other ways to obtain Blaziken.
3. Greninja - this is not a true paywall, but it is certainly leaps, bounds, and quicker to obtain by spending any amount of money in the game.
There are other ways to obtain Greninja, or it's base form Froakie via shards in these places:
1) Mystery Shop (the van which appears after spending stamina)
2) Shard Dungeon (one of the daily dungeons)
3) Shard exchange events
So you've enjoyed your time together with your Geodude, but you finally got yourself an Aggron, congratulations! Unfortunately, Geodude may not fit on your team anymore. Does that mean all the resources you spent on Geodude has been wasted? Certainly not! The game has a Rebirth feature which allows you to reset your Pokemon/items back to it's normal state. Currently, the Rebirth function does not return any materials (duplicate copies of Pokemon or Pokemon/Universal shards) used to star up your Pokemon.
To access the rebirth function, simply hit Decompose in your Pokemon page.