Well, actually...
Your comments cleared up your question for me I think. I came from AI War 1 as well, so the fleets were a little confusing for me the first time I saw them. Let me try and explain how I handle them a little better and how I use them.
I've found the fleet mechanic both a blessing and a curse, especially being used to normal control groups from other RTS systems, and/or AI War 1.
With AI War 1:
You could set space docks up with groups and selectively control which ships were built there. They would get added into that group automatically. You could also create custom "Task forces" from the main fleet blob. Give a subset of them a special number to control them and away you go. This was similar to how other RTSs used control groups and was similar implementation.
Now, with AI War 2:
Think of the fleets as the Intra-Galactic warp gates from 1. Your factories build the ships, and they warp right to the fleets. Now, think of the fleets as permanent control groups. You set a fleet to a hotkey, every ship that is built and "warped" to it becomes part of that group. So, in essence you still have the control groups, just every one has a dedicated transport.
Now for an implementation...I'll use a couple examples from the game I just finished.
Take the "Chop Shop" brigade, that single fleet where I put several groups of saws in it. I used it to drop right on top of guard posts to knock them out while the rest of my "blob" did whatever. In AI War 1, it would be several assault transports control grouped up and doing the same thing.
The "Boom Boom" fleet. A fleet with only Siege Frigates. I wanted to control them against specific targets without affecting anything else. So, they got a custom fleet group all to themselves. AI War 1, I'd give them their own control group number and do the same thing.
If I wanted to split up a fleet...say I wanted TWO "Chop Shop" fleets and split the saws between them. I'd build a custom transport and move some saws over. Then I have two hotkeys...one for each group. AI War 1...separate space docks, or highlight Ctrl+# to do the same thing.
The WEAKNESS of the fleets however...is that if you want to create a new control group on the fly from ships in two different fleets during a battle. AI War 1 it's easy, you can't do that in 2.
Does that help clarify things? I can try to work something up from my in-progress saves...maybe through screenshots or something on my thought processes when I setup fleets?
Don't forget you can build those custom fleet transports. You are not stuck with the 4-6 or so you capture across a game.
The only change I wish we could make...or if it's there I don't know where it is: When you select a fleet to move it somewhere, I want an option to NOT have the transport move as well. I may want the transport to stay "Parked" while the units run around