Let's face it, a million units all over the place is annoying as hell to clean up. If I wanted to clean something up, I would clean my apartment, not a game AI spamming trash all over my solar systems
Early game it's fun fighting since the numbers are low, but while the strategy and tech evolves... battle stays mostly the same. If you could somehow make end-game battles sectorwide, instead of hexwide that could solve a lot of the problems defensively and required attention to details. Speed should be faster, weapons better, so it makes no sense really to keep battles at one hex throughout the game. If you made tactical positions more important with improved tech (moons, planets, asteroids etc.) you could implement some strategy in tactical battles for late game as well as hopefully get some defensive advantages instead of just passive bonuses.
I am just throwing an idea out here, I started playing GalCiv2 after the sale, and it's great fun, but the battle system feels lacking come late game. It's like civilization games, and the Panzer General direction in Civ5 did not work as well as I hoped sadly, so hopefully you guys can bring some fresh ideas regarding this issue with Galciv3.