I trash them if they are not good or in a way a collection piece. I kept the best shiny Squirtle with and without glasses, another 2 similar Wartortle and of course a few such HC Blastoise. I also kept a CP10 shiny Charmander and if they had a CP number I liked, like 77 or 64. All the others end up transferred or reserved for friends that didn’t manage to play or were unlucky that CD, and only under explicit demand.
What to do with extra shinies
I know a lot of people here will say that theres no such thing as extra shinies or whatever, but I like to keep my box clean. I like to keep at least one of each version and evolution stage. But beyond that I don't know what to do with them.
I feel bad transferring them, but I also don't see myself spending the 20k or 100k dust to trade them to someone. Isn't 10 shiny squirtles or charmanders too many?
Answers
Before we knew about trading, I kept one for each evolution stage and trashed all excess shinies.
After trading I've kept all of them in case I ever feel like using them to complete my dex but I was wondering how many of CD shinies I need for that. Seems to me that they're common enough that they're not worth much, meaning 1-2 for trading would be plenty since it'll be rare to find a person who actually wants them.