Let me be more clear on why I wouldn't use the average of any system/section whathaveyou: It frankly makes no sense. It'd be more logical to just add them together, and even then that doesn't make too much sense to anyone who thinks too deeply on it. What would make the most sense would just be to retain the HP of each system and the Hull...when the hull breeches, damage then flows to whatever section was behind that taking away from that section. As is, for some reason the HP of a system at the rear of a ship affects the HP of a system at the front. While this may be a step to streamline, it's one that can end up causing some rather confused situations later on down the line, especially considering how sections can be sealed (a practice that's been around since preWWI that I don't see going anywhere) from each other/ship possibly blown in half and the like.
As for the acceleration I was talking about, it would be fairly simple to implement: rate each engine in terms of megagrams per one unit of acceleration. For the engines used for yaw and attitudinal controls, measure it in megagrams per degrees of arc per time unit (whatever your turn length is). So for main engines, you'd just have a little table listing the different engine choices against the acceleration rate for various mass levels.
In game terms, this all means just keep track of the mass of the ship, when it hits a certain point, they get -1 to their acceleration rate, next higher point a -2, so on and so forth. Then do something similar for the maneuvering engines, but take off degrees of arc (which can be kept simple by keeping it in terms of how long it'll take to rotate a given mass level 45 degrees).