I brought this up on another forum, but I think I put it in the wrong spot. So...
1.) It would be nice if all Federation ships could have universal bridge stations. I say this because the Feds celebrate infinite diversity in infinate combinations and the Klingon philosophy has always been shoot it. This would not diminish the uniqueness of ship-types as science vessels would still have superior scannig and targeting capabilities, escorts would still have the superior maneuverability and forward weaponry, while cruisers would still retain their toughness. But it would allow ship captains the ability to further customize their bridge layout.
2.) It would also be great if one could upgrade bridge stations. One upgrade would switch a station from being Ensign to Lieutenant.
Under the current setup a Galaxy-class vessel has Tactical: Lieutenant (1), Engineering: Lieutenant (1), Commander (1), Science: Lieutenant (1). It would be nice if the ship came with 4 universal bridge stations all rank Ensign, and through a select number of upgrades one could specify which stations had superior abilities. In this case the Galaxy-class would have 5 upgrade slots. Keep in mind it takes 3 upgrades on one terminal to switch it from an Ensign to a Commander. You could even set it up so a captain has to select one profession per terminal if they wish to upgrade the station. This would allow for more customization on the bridge and if you allow upgrades on smaller vessels, then they don't become quite as worthless. (I'm not a Miranda-class nut, but even those ships were commanded by Captains).