I disagree, dont you remember that CGI in the Secret opps when the two cruisers went at it? The Plunkett class one bashed away at the enemy ship, not the engines or the bridge, just bashed away at it, and it eventually exploded!
Out of necessity, a large capital ship has enough fire power to waste another. This goes pretty much without saying.
When a bomber that costs 1/1000th of the price, took days instead of months to construct, and only puts 1-4 crewman at risk as opposed to hundreds, why would you optimize your fleet for Jutland style battles?
Wing Commander was a smart enough game and universe to know this rule.
Now if a capship is caught off-guard by another, or you have a von Clausewitz 'concentration of force' scenario on a particular objective (like Earth, Sirius, McAuliffe, Kilrah etc...). Then I could see more direct capship confrontation.
Also, our perspective is that of a carrier pilot. Throughout the war, Confed only had 50-60 carriers (at the absolute most) at any one time. We may also assume that the state-of-the-art Heavy Fighters and Torpedo Bombers would be assigned primary to these ships. Most of the Cruisers and Destroyers would probably be assigned point-defense ships and other lighter fighters. There were several thousand cruisers and destroyers on both sides. So, from our perspective, our escort ships don't need to engage other Capships, we can do so in our Sabers, Longbows, Raptors, etc...
Now if WC simulated the main character as a pilot on board a DD or CC (or even a base), I am sure we would see more direct capship vs. capship fighting.