First off, there are a LOT of adoptable communities. You seem to be focusing on JBDs, which is fine.
BAWWw messages:
Yep. Super annoying, spammy, and whiny. Usually, you just ignore that stuff. Some artists will put on their adoptable not to do that on that thread, ie the front page or the winner announcement. If the post is made to actually make someone feel bad about winning, then report it to a mod (of the adoptable or of CS)
It's actually a JBD rule "★ Do not complain if you don't win" So if you see any blatant complaining, PM a JBD mod.
I have no idea if this is a rule for kias, makotles, etc.
Blatantly asking for nursery batches:
Yup, also annoying. If it gets to the point of harassment, report it. Most owners of the adoptable parents will simply ignore the beggars, or put them on a "definitely not getting this baby" list. I don't think a horde of people crossing their fingers for the baby going UFA has
ever actually influenced the parent owner's decision.
Applying for staff customs:
I have no idea what you mean. Kiamara staff have given away their custom slots to friends before, but I've never seen anyone who's actually involved in either community attempt to "apply" for one. Some examples would be nice.
Cliques:
I'm afraid I don't have much input on this. Some people have blocked lists and actually cannot see others' posts on the chat. Cliques happen in RL, on CS, and everywhere. Sometimes it's just a matter of making friends, which can be more difficult for some people. Not sure what can be done to fix that or force everyone to be inclusive. Food for thought though...
And that's just the jbd community. I don't know about you, but I'm glad we don't have trolls going around sending each other venom-filled hate messages and treating each other like garbage. (though on ask.fm, there has been a troll going around in the last few days)
As for "not as friendly/positive as they seem"
Is anything?