I had some ideas for a Galactic Civilisations 3 combat model. Basically a random wishlist on my part, but I figured I might as well share it.
1) Simulated combat instead of rule/random number based combat
This is to say that the battle viewer wouldn't just be a fancy cosmetic layer overtop of a fundamentally rule based combat system, but a simulation of the fight given the ships and their equipment. This would NOT involve tactical combat... the problems with that have already been discussed. The battles would be handled exclusively by the AI, so that the player gets no unfair advantage over the (by necessity) limited tactical AIs.
This would mean a newtonian physics model for ships, turn speeds and firing arcs would be concerns, and projectiles would be simulated. Combat would no longer take place in turns, but would be utterly constant: weapons with high rates of fire would become possible.
2) Expansion of the weapons technology
The split into multiple different weapons types is an awesome decision on stardock's part, so lets expand on that: the beam, mass driver, and missile lines would be split into sub trees for various purposes, with differing range, fire rate, damage, and space considerations. I would propose that it be three branches: heavy, medium, and light weaponry, with their corresponding range, damage, and space concerns. The reason why will become apparent in a moment. These three branches would likely each correspond to different subtypes of beam, missile, and mass driver weapons. Missiles might have, in order from lightest to heaviest, kinetic kill weapons (basically guided mass drivers), guided missiles, and heavy ordinance missile weapons (ie, weapons that have exceptional yields, like antimatter weapons).
The reason for this complication of the weapon types is twofold: for one, lighter weapons are easier to load on smaller ships, are cheaper, and can fire at faster rates, while heavier weapons can strike longer ranges and will do huge damage with the initial hits. The heavier the weapon, the greater the effectiveness in the opening of the fight and the more effective they are against heavy, slow moving ships that they can hit more reliably.
3) Further combat specifications in ship design
The second reason is the ability to specify firing arcs for weapons as you mount them. They could be fixed, where the ship has to face the target (its own manuevering abilities come into play, meaning that light ships fair better with this), and the space requirements are smaller. Alternately, they could be turret mounted and be able to strike at any angle, at a substantial cost in space. With the heavy weapons, the space for turret machinery would be prohibitive... good luck mounting your ship length mass driver on a turret! There would also be a compromise somewhere between the two, where you could gain a limited firing arc without a prohibitive space penalty.
The mechanic here is pretty obvious: small ships can fire fixed weapons with little penalty, but larger ships can only use their big guns on targets that don't move much. In order to fend off smaller craft, they either need fighter escort, or smaller weapons on turrets.
This provides more opportunities to sieze upon flaws in your opponents battle strategy, and ensures heavy variety in fleets.
The other factor worth mentioning here is that the battles would be INCREDIBLY cool to watch.

4) Combat doctrine
This is something I'm a little iffy about... it might be better to have ships automatically choose what doctrine to follow. Regardless, there are three main strategies I can think of for individual ships: active pursuit (rushing to get into the thick of battle), lateral movement (circling around targets in an attempt to stay at the edge of battle), or standoff tactics (actively attempting to maintain optimum combat distance). Regardless, individual ships would need to choose how to play the game. One fleet strategy might be to send in the light ships to tie up everything at close range while the ships with big fixed gun emplacements hold off and snipe at the opposition. Then again, it might be the only real optimum strategy, so it might be better to leave that in computer control and keep the micromanagement away from the player. I dunno.
Anyways, your thoughts on my incoherent ramblings?