Okay, okay, I figured out how we can handle some of the refit issues: some of them.
So, seeing as how the tier four ships got refitted and have special powers, let us extend the courtesy to the other ships in a refit option.
Miranda class - The "They knew exactly where to hit us" power
Saber class - Engineering buffs out the wazoo! Remember that this ship was used by SFCOE
Excaliber/connie-refit(refit refit?) - Kirk Luck!
Nova class - There was that voyager episode where they abused a lifeform to up their power supplies. How about a power surplus based on the research done (though modified to not be so... un-Starfleet about the whole ordeal)
Akira - carrier/torpedo unloader
Stargazer - ability to make a last minute warp out of any dreadful situation, though this need not push it into a separate instance, but give a warp like appearance
Olympic class - Healer like nobody's business