Firstly I would alternative killing the easier MH/BT bosses with Kael'thas attempts. Allow people the pleasure of some easy loot and new content whilst still clearing the T5 instances.
Loot ... I wish there was an easy answer. We use a modified /roll system prioritised according to class and raid attendance. It has served us well but there are times I think we should have gone the DKP route. However, it takes just one selfish act to make you realise that there is value in DKP as people will only roll/bid for items they really want.