The issue with the second boss isn't the captains he summons, it's the actual normal drakes. Ocassionaly the normal drakes agro when the Captain attacks you. This can be solved by killing all the low flying drakes before pulling the second boss though.
This has been around since the instance released and is by far the biggest cause of any group wipes/deaths I've seen.
My rogue que'd random once, before the first Centrifuge Constructs were even pulled, we had lost 3 tanks and 4 healers that all qued, joined and dropped before a word was said.
I am, however, a bit annoyed that you can only get the Blue Drake by random queing (I've been dropped in there quite a bit recently and have about 30 clears of the place now, most being with the new system though) and would actively que for it if I could get a shot at the blue drake, but I guess I'll just spend a weekend/etc going for a luck of the draw...