There should REALLY be some kind of prison island for all the caged dragons that are clouding up my desired layout....It could be just my OCD but I like to lay out my habitats a certain way and now that these cages (that I will NEVER purchase) keep popping up, I can't set up my stuff the way I want to

If you know you will never purchase them, then remove them. You do this just like you remove any other obstacle on the islands, bushes rocks etc. Bottom right of the screen when you click the cage.