As I see it, Sins of a Solar Empire is very similar to Homeworld 2 in that aspect, except it brings it to a higher level. In Homeworld 2 you fight one map, in Sins of a Solar Empire you fight galaxy-wide. And where Homeworld 2 need you to control the ships on a finer level, Sins of a Solar Empire has a smarter AI behaviour and you focus on the war on a grand scale.
The only issue I have with this is that in Homeworld 2 I care more about my capital ships, as they're much more expensive to build and it takes a long time. They become your pets. In Sins, I don't feel for my units. I just build them and send them off. I really hope to get something in Sins that I can feel for like that, something that feels special, somehow. If people understand what I mean. Even if it's only a command ship or whateer it is, something that I can only have 1 of. something that's mine, and personal.
Finally someone understands me, and that's where my flagship idea comes, see post for flagship. Since it is supposed to be your personal ship you can customized completly...oohh yeah.