Nonetheless, they did. The New Republic armed forces made use of a large number of captured or abandoned Imperial Star Destroyers (hey, it's cheaper than building new ships), including the Super Star Destroyer Lusankya. They even named a one after Mon Mothma. And, in fact, they used the orbital bombardment capabilities of the ex-Imperial ships on the Yuuzhan Vong.
Towers: The problem with this old argument is that you can go back to where some ILM guy scribbled "radar dome" on his notes, or you can go through several games and books where the domes are referred to as shield generators. Or you can watch the movie where we see a dome blow up and then immediately cut to an officer yelling, "Sir! We've lost the bridge deflector shield!" It's not really a big deal...but most people have been thinking of them as shield generators for long enough to make that the prevailing wisdom. That "technical commentaries" guy has got way too much time on his hands and he says funny things sometimes. Now as far as Empire at War goes, giving the ISD a second shield generator hardpoint would make it a lot tougher. Maybe the turbolasers should fire more shots per volley, too.
Mon Calamari cruisers should be weaker than Imperial Star Destroyers, but should be faster and more maneuverable. The fact that ISDs were built as dedicated warships does mean they will be superior to a starliner at approximately the same technology level. The ISD will have all the necessary support structure for military hardware: weapons, power systems for weapons, armor, a hull designed to take a pounding, etc. The thing about military ships versus cruise ships is that one is designed with battle in mind first, and people in mind second (ever see how cramped the crew quarters are on a submarine?). Cruise liners are the other way around. The Mon Calamari may have been able to adapt their venerable starfleet, but those ships will not be able to go toe to toe with Star Destroyers.