I just started playing Sins a few days ago, and I have to say I really love the Empire tree and nearly everything about it. Some of it takes a little getting used to, but it's very well done overall.
I have a hard time, however, managing fleets and groups the way I would like, which is basically to make each fleet equal a group. It's possible, by always assigning a fleet to a group, but it feels awkward. It's hard to identify in the left-hand tree which fleet is which group. In addition, it's hard to keep a fleet as a single group over time. I create the fleet and the group together, but as I try to add or remove ships I frequently end up with some parts of the fleet not in the group, or vice-versa. Then, if I select the fleet by using the group hotkey and give an order, not all of the ships get the order. Finally, while it's sometimes nice to have the ability to keep the same unit in multiple groups, more often it just adds confusion (perhaps because I'm not used to that feature). I think that if I wanted to be able to control both large and small sets of units, I would do that by using fleets with sub-groups, or groups of fleets, not overlapping groups.
My preference (if I were designing the UI) would be to display fleets in a separate tree on the right-hand side of the screen, and combine the concepts of groups and fleets, so that fleets always have a number and a hotkey. Keeping fleets separate would also reduce the confusion of having ships show up in the left-hand tree under both the fleet and the planet they're currently in.
Am I using fleets and groups the wrong way? How do you guys manage your fleets?