To my understanding what made her special was the mixture of military and science departments. After all we see strictly science vessels in movies like TSFS, and that doesn't contradict anything in TOS. So, for me the logical conclusion is that the Enterprise is a special design because she was built to do a little of everything. Capable of performing combat and science duties at long ranges. However, up against a class specially designed to do one or the other, she's likely to fall behind.