Yes I agree we need a way to use more than 6 pets - some kind of pet warehouse where you can store your unused pets and a way to move them to your pet slots. I could simply increase the amount of pet slots from 6 to 12 but it's not really a solution for those that want to collect a lot of pets, and there are quite a few technical reasons why I have not done this.
Ideally, I would like to have some kind of pet collection system - similar to the tarot card book, where you can store pets and easily choose which ones you want in your 6 pet slots.
It's on my list of things to do, and has been for some time. I'm just not sure how best to go about implementing it yet. I don't particularly like the idea of turning pets back into a scroll or DNA though. We need some kind of collection system.