I haven't read through all of the posts in this thread, so sorry if this has already been requested:
One thing that's always bothered me is the implementation of the Naval Organization tab in the Task Groups window. Don't get me wrong, I absolutely love the idea of it, and this is the only 4x space game I've ever played to even attempt anything like it, but it could still use some work. Specifically, being able to issue commands to all the ships in a branch (including sub-branches) when they're in different locations. I tend to organize my navy in an Armada->Fleet->Squadron->Individual Ships fashion, and I'm constantly separating and recombining task groups based on my needs. Being able to issue a single command to an entire armada or fleet to assemble at a specific location when individual ships are in different systems would be hugely beneficial to me. I admit that there are ways to accomplish this currently, but doing so is fairly cumbersome.
Thanks for your time and consideration.