IMO, a partial cause of the problem is the predominance of shields over armor. Shields automatically regenerate after combat; armor doesn't (except for organic, post-next-patch?). If use of armor over shields were encouraged (better hitpoints/kt ratio?), ships would have to repair some damage.
Another part of the problem was posted in another thread. Frequently, ships are destroyed in single combat turns; if ships could Last for an entire battle (higher hitpoints or less damage per weapon), then each ship would have a higher chance of being damaged.
The use of engine- and weapon-damaging weapons greatly increases the odds of crippling your enemy's fleet--except that crippled fleets tend to die in a single combat round. If only they weren't so expensive.

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The Unpronounceable Krsqk
"Well, sir, at the moment my left processor doesn't know what my right is doing." -
Freefall