I think the retrofit ships are too attractive to use over the base T5 ships. These are supposed to represent the pinnacle of Starfleet tech, yet the Sovereign is overshadowed by the Excelsior, the DSSV and RSV are overshadowed by the Intrepid, and so forth.
So here is my proposal for the non-retrofit T5 ships:
Assault Cruiser: Remove tactical Ensign, convert tactical Lieutenant into tactical Lt. Cmdr.
Star Cruiser: Remove science Ensign, convert science Lieutenant into science Lt. Cmdr.
Deep Space Science Vessel: Remove engineer Ensign, convert engineer Lieutenant into engineer Lt. Cmdr.
Reconnaissance Science Vessel: Remove tactical Ensign, convert tactical Lieutenant into tactical Lt. Cmdr.
This would turn the base T5 ships into the advanced 25th century ships they're supposed to be.
...But wait, I'm not finished yet! I also think the Galaxy-R, Intrepid-R and Defiant-R need a refit. I think they are far too specialised when they might be better with a little more versatility thrown in. Bear with me on this one.
All retrofit ships: Change Ensign boff to universal.
Galaxy-R: Add tactical console slot, make saucer separation a removable engineering console.
Defiant-R: Add science console slot, make cloaking device a removable tactical console.
Intrepid-R: Add engineering console slot, make ablative armor generator a removable science console.
Now the retrofit ships are unique in their ability to mimic the current configuration of the stock T5 ships, with a real drawback to their primary mission focus if they use their special ability. The Galaxy-R can now match the base damage of the Sovereign or Excelsior - but if you want to turn like an escort, you'll have to sacrifice some tanking ability. The Intrepid is now slightly tougher, but if you want the ablative armor, your science powers won't be quite as strong as they otherwise would be. Ditto for the Defiant and cloaking vs weapon damage.
But what about the Excelsior, Nebula and D'Kyr class?
I think the Excelsior is pretty well balanced as it is. It's as tough as any T5 cruiser, but far more agile and its combat ability would still be on par with the Sovereign if the change above were made. But its tanking wouldn't be quite as effective, and it has the agility and transwarp as a tradeoff.
I think the Nebula class needs a boost in the form of a 4th Forward weapon slot. This would make it truly unique amongst all science ships without resorting to making it like the others with a different skin.
The D'kyr is an excellent science ship, doing for Science what the Excelsior does for combat. I think it should remain unchanged.
I'd really appreciate feedback from everyone on this idea, but I hope the Cryptic staff see it too and say something about it.