Overall, I have mixed feelings about this section. I kind of like it, but it is one of those big departures that I'm not sure is better than what is there now.
On ship upgrades:
Ships should have to return to friendly territory to upgrade with new tech. Just go to a planet you control and hover your fleet nearby the station, perhaps they could have a small Refit Radius. You could have little drones come out from the station and do the refit (like the mining drones from that other thread about salvage).
Please make sure I CAN'T fly my crappy / expendable fighters into place, then upgrade them magically and instantly from my planet across the galaxy, right before the fight. It sounds like you're saying we will be able to do that, and that seems exploity.
On homogeneity of ships:
I do actually use my MkI ships for small operations off of the main fleet. I might select my MkI Bombers, hit L once or twice, and send that expendable strike force off to slowly bombard some target while the rest of my fleet heads for the main operation. I might grab half my MKI Fighters and send them on a suicide mission to delay an intercepting enemy fleet.
If they were all completely homogenous, I wouldn't have any expendable ships. Neither of the above scenarios would be as practical.