First, fleet view.
I create a fleet, hotkey the leader for easy access, and the bloody empire tree switches to the planet they're in, which is generally cluttered, and may not even show what I'm after if the fleet is in transit and separated. It's definitely not what I was planning to be looking at.
The selection based tree is nice, but fleets should most definitely have priority in what it looks at, having to collapse every planet to keep it stable defeats the purpose of having the tree in the first place. If not, having an off button for the selection based empire tree would be a close second, it's driving me mad as is.
Second, fleet creation and management.
I waypoint a shipyard to a fleet, the new recruits join the fleet. Or not, some of them just sit around sucking their thumbs. I fail the grasp the logic in forcing siege frigates and disabling cruisers to follow the leader instead of actually join the fleet. If I don't want them in the fleet, and there are valid reasons for both, then I probably don't want them following the fleet either and can click somewhere else for my waypoint. Maintaining a steady resupply is outstandingly simple, unless you want ships that wont bloody join it, then you have to micromanage them, which changes their ordering on the empire tree, and can be fairly complicated with multiple fleets in the same place having their own coat tails following them.
Third, group movement with fleets, buggy?
They're rather staggered, suboptimal in deployment generally. When they all popped in simultaneously in beta it was real nice, dispersed targetting and optimal effect from your fleet composition. Now it's often rather messy, even with ships dying before the entire fleet has come through despite being together when the movement order was given. They almost pull off the coordinated jump some of the time, and others I'd have been just as well off by collecting them at some point and just moving them without group move at all.