I agree, but I would like to be able to upgrade my fleet escorts as I would the Vindicator, as some ships would fall out of favor with newer designs, it would be nice if even the older models of ships have a (albeit small) niche. Customizing escorts would also go a long way to strengthening the RPG element of the game, and creating a bond not only between you and your ship, but also your entire fleet.
What you're referring to was definitely an element of SC1; you did not have a flagship, but if any ships in your fleet visited a world with Precursor artifacts, they would automatically be integrated and provide bonuses to speed, firing rate, crew capacity, battery power, etc. Of course, these bonuses were completely random and you'd never know which ship might land on an upgrade or what the upgrade would be. Having finer control over which ships get the upgrades you discover would totally rock.
I've been an advocate for acknowledging and expanding upon some of the elements from SC1 that didn't get carried over into SC2, and this fleet upgrade dynamic is definitely one I think we'd all like to see. I have a feeling some people who only know about SC2 and who didn't even play SC1 might not have even known about it.