I would love the option to scale up into huge arenas - I do like the longer games too.
I would love to see some sort of leader system. Not like MOO2, more like Hearts of Iron.
Basically just a database of names and they are assigned to every division built, every ship etc. Each leader has some form of Skill, experience and Rank. Same as ship experience each captain can gain until he reaches next level(skill increase) or if you chose to promote him, trade it in for Rank (Higher Rank means they can control more units, Captain controls 1 ship, whereas an admiral can control 30 ships for example, exceeding it would be detrimental).
The Skill could be used for a combat modifier (especially in autoresolving). On creating fleets and auto-assigning available personnel, it may be worth promoting an experienced captain, maybe I have a favourite heh. I think this adds very much to flavour, we can leave it to do its own thing but we can delve into it to tinker with some of the whos-who in your army/navy.
Furthermore, possibilities of extending this go into news/flavour reports naming the individuals, or events - for example royalty of your empire joining the navy forcing you to not needlessly expend that fleet in your next foolish venture. If you have a leader Rank = maximum number of ships controlled value then tech options to expand this number become a bit more desirable (ship datalink/neural links techs etc). Surrender may require you to hand over specific admirals etc etc
..maybe getting a wee bit too much now for something already in production but the base idea alone would add some nice flavour.
