@Tequila
I like the idea of Limited Adoptable Space, it will be implemented in Mys v1.4.0 guaranteed. I am not sure a team limit is necessary for version 1.4.0, it will come in handy for Mys v1.5.0's battle system though as you cannot use all your adoptables in battles. The adopt-box idea is quite tied to limited adoptables space, I will consider it for sure, or maybe apply to items/inventory too.
For The Nests/Litters feature, is it just like a background for adoptables? I am sorry I dont quite get it, sounds interesting though. For the Ad system I will need a better description too, maybe a picture/drawing of how you want the ads to be displayed on the site's layout/screen?
Stats is a big topic, it is planned as main new feature for Mys v1.4.0 and I want it to be as flexible as possible. Maybe I will define some basic stats like HP, MP, Strength, Vitality, Intelligence, Spirit, Dexterity, but users can give them special alias(such as SP is to MP, Magic is to Intelligence and so on) which will actually be used as displayed name/attribute for adoptables when you view their stats. Admins will have full control of how they want the stats system to be, each stats can have its own formula of growth based on adopts species, level and some random numbers. You can specify a base stats for different specifies, which will be useful to diversify the stats among each adoptable species.