I've been thinking about how ship refits could work. Part of the problem is that older tier ships have inferior hull, shields and weapon slots. My idea is thus: add a Warp Core equipment slot to the ship.
The Warp Core provides the ship's energy and the system would be set up to provide a regressive benefit with ship tier. You'd put a Mk IV core on a Miranda ship, and you'd receive a boost to your weapon and shield power. You could have new Warp Core loot, with benefits to power transfer rate, or sub-system power etc. Furthermore, you could use the Warp Core to determine maximum warp speed in sector space.
It wouldn't make any difference to Bridge Officers or equipment slots, so it's not a perfect refit alternative... but I do think it's an approach that makes sense.
I would like Warp Cores added, where you get more power output out of them. And them not be "one size fits all". After all, you're not going to see a Defiant with a Galaxy's Warp Core.
Well, the Defiant was said to powerful because it had a high performing warp core [on par with a Galaxy] built into a small frame. If anything its primary design flaw was that it was overpowered... which in turn gives another balancing possibility:
For every point of power in a subsystem above the ship's safety rating, give a set - small - chance of having that subsystem fail. Shields can miss a regen cycle or have a power reduction; engines can stop; weapons can fail; aux can be drained. That way you can have a Sovereign class warp core in a Miranda, but you've got to take into account a constant risk of ship failure.