I'd be all for complaints about asymmetrical ships if they weren't just thinly veiled "in my opinion I hate them", there's just opinions in what you wrote, no facts.
At best one could argue they'd require the thrust vectoring to be aimed through the center of mass. But then the same can be said of symmetrical craft and nobody complains about the Anaconda's thrust not lining up with it's center of mass. There are only two ships in the entire game that shouldn't be completely disabled if they lose one of their primary thrusters, the Imperial Cutter and Asp Scout, both have one main thruster right in line with their center of mass.
As an aside, most real world spacecraft are asymmetrical because it's cheaper and lighter to use only 1 of something instead of trying to create symmetry. Simply align the thrust so it goes through the center of mass. Try it if you have access to kerbal space program.
http://i.imgur.com/tKGA70y.jpg