I just have to say this; as far as scroll goals go, I intended at first to obtain 5 of every gender/colour for each breed (as adults, except unbreedables). As time went by, I found myself having uneven numbers of several breeds (most of which are actually commons), so while I myself am pretty flexible when it comes to scroll goals, most dragons "lose" value to me, once I have obtained what I consider to be my goals. I have a couple trios "over" the limit, but that's because I haven't been able to trade them away before they grew (sure, I could have gifted them, but I was after something specific.)
As for biomes? What I would like is to see a separate biome for Pygmies. I like Pygmies, but not everyone does, and they sometimes tend to sit and block for the rest of the eggs in queue. It's not like pygmies are rare, so I don't think putting those in a single biome would throw things too much out of what? It could be "Pygmyland". I'd also love to see unbreedables (dinoes, chickens, cheese, papers etc) in a separate biome, but that would defeat the purpose of those being classified as rare, I understand that.
Overall, I am pretty content with how the site is run, and I don't think there has been a single change I've not liked. I'm one of those not too hard to please.
Edit: Sure, I'd like to see something extra implemented for each trophy level you achieve, but that wouldn't affect my playstyle (unless it included opening up more egg/hatchling slots. It's mostly the eggslots I fill anyway, not the hatchieslots.)