While I prefer a fleet of uniform tech level (e.g., all low-tech or all high-tech), either on my side or the AI, there are some roles that can be done only by one epoch, and no self-respecting warrior who wants to win a war will limit his choice of weapons just because they feel wrong or look ugly. If the most effective fleet is a blend or mash-up, then that is what will be used. Some call this min-maxing and/or munchkin. Well, min-maxing wins fights.
Fighters: If I want to kill things, I use Broadswords and Thunders. If I want a decoy to soak hits until my Odyssey flagship arrives to utterly destroy whatever, I use Xyphos.
Frigates: I use a variety depending what I want to do.
Destroyer: As a flagship, there is no substitute for the Medusa. It is powerful enough to solo any fleet and fast enough to catch up and kill frigates. It is true all-purpose ship. It is also the only destroyer with decent burn speed. If I pump up Navigation high enough, I may give AI Enforcers to pilot. Ballistics are generally superior to energy weapons. For carriers, I would avoid the Condor at all costs; the only way it can fight is Pilum spam. Gemini can at least fight in a pinch. For freighters, Buffalo is just bad. I would use either Tarsus or Mule. Tarsus because it can flee with burn drive. Mule because it can fight.
Cruisers: High-tech cruisers stink - none of them can focus-fire more than two blasters, and thus, do not outperform Medusa significantly enough to justify bigger profile, greater logistics cost, and slower speed. The Eagle, with max Combat and Technology, can mount and focus-fire three blasters (and shield-buster ballistics) and smash fleets faster. Thanks to maneuvering jets, it can be fast when it needs to. As for carriers, Heron is the best.
Capitals: If I feel like using only one ship to battle, it is Paragon. If I want support while I zip around in a smaller ship, Onslaught. Low-tech also has the only superfreighter (Atlas) in the game.
Generally, while I prefer high-tech ships, the CR costs for most of them are so bad that I avoid using them as AI escorts. Often, I need disposable Lashers for the AI to use so that I can fight more before running out of CR.