The Inquisitor wrote:
Would you rather face one massive guy in a fight or three smaller faster ones?
That's what the argument boils down to, but it points to the opposite of your conclusion.
I'd rather face 3 smaller, faster guys, especially if I was bigger than any one of them myself. I can target one guy exclusively, and knock him out of the fight. Now it's me vs 2 smaller, faster guys. Again, target one guy and ignore the other (and yes, take a beating from him in the process, but I'm bigger/stronger than him). Now it's me vs a smaller, faster ship.
Pick the Mother ship the first time (by knowing that or dumb luck), and you only have to beat one section. Might even get to keep the other two components as spoils of war, if you can take control after the mother ship is dead...
Makes the one big ship much more dangerous, as well. Not only wasted space when connected, but you've now got a lot of extra fuel tanks, torpedoes, etc stored all over the place, so a lot more places where taking a hit means catastrophic damage...