So,
I notice that one poster said that my proposed system is flawed because defense would obviously run away with the game, and another that swarms of all-attack escorts are the way to go. *grin* This sort of "consenus" suggests that my system might have something to it.
On to some specific issues.
1) Complexity: What I proposed really isn't very complex at all. However, I described *all of it* in sufficient detail for a programmer to just code it, as though from a design spec. (I didn't spec out a UI for fleet composition, but some straightforward implementations come to mind. There's also some AI work needed, because forming and reforming fleets on the fly becomes incredibly useful; that's less straightforward.) In some ways, this system is more straightforward. For example, a player doesn't need to think too hard to figure out which ship in his fleet will be attacked first.
2) No incentive to research good weapons: Hmm. An example was given comparing Phasors to Psyonic Beams, suggesting that Phasors are better in my system. So. A Phasor is size 7+4%hs and a Psyonic Beam is size 8+4%. In the example provided, it is suggested that a ship can either contain 8 Phasors or 2 Psyonic Beams--which is clearly not the case. The ratio is close to 1:1, although the PB ship will cost much more--as it should.
3) Fleets of all-attack, all Escorts are the way to go: I think said fleet will not enjoy an encounter with a fleet of Escorts with some defenses protecting Warships with all attacks. In the proposed system, defenses are *good*.
4) Defense will run away with the game on large warships: This, from the same poster who suggested #3! Defenses *should* be good. Here again, however, I believe that determining the optimal ship is not simple. First, low-tech weapons are not efficient for size compared to more advanced versions; you cannot fit 2 Phasors into the same space as 1 Subspace Blaster! Second, a ship that loads up on all defenses and only a single weapon is not necessarily going to do well against a ship that is slightly less well-defended but has a second weapon of the same kind. Third, battles involve fleets, which might do well to contain ships of different kinds.
5) Fleets ought to be damaged after a combat: Why? The timescale of GalCiv is so vague anyway. Does anyone really consider each game turn to be a week? Maybe the ships were repaired between combats. As for attacking a damaged fleet, that fleet will probably have lost ships from the previous combat, weakening it. And, if it did not, maybe the initial attack was a mistake! Swarming advanced ships with neolithic canoes becomes less useful; you might get lucky but are more likely just to scratch the paint. Keeping up with technology matters more. Finally, the AI isn't very good at dealing with being swarmed, or at swarming; reseting damage between combats ameliorates this. And more than finally, tracking and swapping out damaged ships gets really, really tedious.
6) Realism: Hmmm. Realism. Sort of like the one where in the course of a few weeks, billions of taxpayers appear on newly colonized planets. Or the way I can upgrade a ship that's in the middle of nowhere. And if my version of repair is unrealistic, then what about overhauling a ship in the middle of nowhere, and for no expense? Or sending the money or insight for an anomaly found on the other side of the galaxy back home (where the bonus is assimilated and put to use all in a single week)? Or loading two billion people onto a single ship, sending it to an enemy planet a sector away, training them as soldiers to get a bonus, killing their enemies to the very last child and then resettling the planet, all within the week? ;/
7) Rigorous analysis: I haven't crunched the numbers in detail.
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A Variant:
Kill hitpoints entirely, leaving the rest of my proposed system intact. However, any ship other than a cargo ship can take a number of weapon hits equal to its logistics cost before being destroyed. Experience applies to a ship's attack and defense, not hit points.
Under this variant, repair rate might do one or both of the following:
a) At the beginning of each round of fleet combat, every damaged but undestroyed ship has a chance to recover one level of damage. That chance is equal to the repair rate.

Rather than having damaged ships emerge from combat unscathed, a ship has a chance to regain one level of damage each turn based on its repair rate. (I still prefer damage to reset fully between combats.)
Hmm. I think I like this variant, with repair rate as (a), as much as my original. Hull size now acts differently from ship defense. Building ships with only attack is obviously a bad idea except on the smallest ships.
Anyway,
Ken