Basically the rule would be to resolve human-human battles first (human-computer battles would only take place if there is no human-human options for that human)
Most of this is irrelevant. No player can manually control more than 1 combat per quantum anyways. I wonder, though, if it is in fact possible to resolve more than one combat at a time if they involve separate players.. for example, could AvB and CvD happen simultaneously?
The entire question is only relevant in multiplayer, and even then, it has been established that a player can only manually control 1 combat per quantum in multiplayer and the rest must be auto-resolved.. Therefore, the maximum amount of time a single player would have to wait around in a given quantum is (Number of players - 1) quanta worth of combat, if they are the last player to go, and everyone else elected to manually control a different battle.
Presumably a player could elect to manually control a combat against an AI rather than a Human if he felt the battle was more deserving of direct control. I would certainly be more inclined to manually control a battle against an AI death fleet than be forced to manually control a battle against a Human scout. I shouldn't be forced into the second combat simply by virtue of the scout being Human-controlled (This could be hideously game-breaking if you were smart enough to send a bunch of scouts at an enemy on and around the same quantum an AI player was attacking them, forcing them to auto-resolve all these important battles and forcing them to manually engage your scouts instead).
As a fairly lengthy example, let's say there are 3 combats occuring on a given Quantum, in a 2 player game:
1) Player1 vs AI
2) Player1 vs Player2
3) Player2 vs AI
Player1 could elect to manually control 1 or 2.
Player2 could elect to manually control 2 or 3.
-If both Players elect to control Battle2, then they will square off human vs human.
-If Player1 elects to control Battle1, and Player2 elects to control Battle2, then Player1 fights against AI, and Player2 fights against AI (controlling Player1's fleet).
-If Player1 elects to control Battle1, and Player2 elects to control Battle3, then both Players fight against AI, and Combat2 is auto-resolved.
The question which remains is, can the server handle multiple combats simultaneously? In the above example, let's say that Player1 and Player2 both elect to fight against the AI opponent (Battle1 and Battle3)... Why shouldn't these be able to happen at the same time? As long as the battles are all summed up and reported to the server at the end of the quantum, I don't see any reason why any player should have to sit around waiting at all.
This train of thought is starting to drift off-topic so I'll leave it there.