premise: I totally love the idea of commanding a fleet without direct control of each ship. A mindless armada is what usually makes good RTS games a bit flat, and that is why they need heavy scripting to generate challenging opponents. So keep up the good work with the AI.
premise 2: I just love that you are bringing the game also on mac, I would have just bought the game for that alone, nevertheless your game actually rocks and deserve what I paid.
Lets get to the point. There is just one thing that is missing about the fleet control: more flexibility.
IMHO, there are too few kinds of "assignments", I'll articulate.
lets pick the escort command. It gives very little options, just light or destroyer (that is actually very open as definitions, given that there is not "light" class and "destroyer" actually includes also cruisers I think). Lets say I want all the fleet to escort my flagship, I cannot do cause the lack of a full fleet escort command. I'm be able to achieve that using a lot of command points, but this is not always a good idea.
Lets expand the theme in at least 2 plausible situations:
first - I have a powerful but very slow capital ship, like the onslaught. My shield is only frontal, that means I'm weak versus fast moving ships that can avoid my frontal barrage and strike at my back (bis'mark

), PLUS I'm very vulnerable to missile attack due to size and speed.
Now in my escort group I need some point defense frigate and interceptor wings for bombers. Aalso a sister capital ship (or equally powerful ship), to bring some additional firepower where I cannot reach with my slow moving mammoth, therefore nullify my weak spots.
second - I have a conquest type flagship, that more than anyone resembles the ship-of-the-line concept. With this I also mean that you are bound to show your wider fronts to the enemy, that means you are a big and easy target. While the directional shields are a flexible beasts, you cannot efficiently protect both your broadsides, and the PD system cannot save the day in front of a combined volley of torpedoes (for examples).
A group of bombers with a single medium ship can easy outmaneuver and destroy you... given they can avoid being destroyed by the conquest mighty weapons in the early stages of the fight. As the conquest commander, more than anything I would like an insurance that while I'm engaging enemies, nothing is going to strike at my sweet spot, or that it not an easy task to do so.
In general, what I need is another rank of assignment, the said fleet commands, that ask every ship in the fleet to follow given orders.
More that that, I'd like the possibility to change the rule of engagement: If I want a close escort, no one should leave my side under any circumstances. Now escort ships tend to chase enemies until they are destroyed, leaving my flagship exposed. I'm talking about making a reliable battle group.
Captains personalities are bound to generate many type of different responses to these kind of orders so I'm not talking about recreating the mindless armada, I'd simply like the idea of a deeper degree of organization.
I'm having a lot of fun beating the missions with better tactics and maneuvers, and that is just bit hindered by the lack of variety of the assignments.
WoT done, thanks for the reading, and GAMBATTE.