I have forgotten which game restricts fleet size... was it sword of the stars? I found that unintuitive and arbitrary, and poorly justified-- an important balancing tool for multiplayer, but annoying.
Sins of a Solar Empire limited both your fleet size and the number of capital ships you could have.
I agree with the OP on all his points. I'd personally like to see fleet coordination get better as technology improves. For example, Travel and fight in formations, travel at the speed of the slowest ship instead of getting strung out as they travel through hyperspace individually, and also jump out of hyperspace closer together as well.
Kushan

