Exactly, Starfleet is designed to face the every-day mundane threats. Orion Pirates, Klingon or Romulan Privateers, the occasional space-born life-form, with the ability to band together to create a unified front on the rare occasions that an all-out shooting war would start.
If they designed all their ships to deal with Doomsday Machines and Naradas, then the Vengeance
would probably had been one of their WEAKEST designs. Plus, a lot of the science stuff would fly out the window, except for being optimized for combat.
So okay, a Doomsday Machine would probably be a doddle then, but woe-betide you dealing with a Whale Probe or V'Ger when you need science to overcome the problem and come up with a solution!