What I would really like to see is Auxiliary Control not being a requirement for an Executive Officer, but instead allow the appointment of an Executive Officer anyway.
A Bridge would then become a special item of which each ship could only have one (similar to how there can be only one type of engine), typically housing both the Executive Officer and the Commanding Officer, meaning both can be killed in the event of a hit on the Bridge, where there is no Auxiliary Control present.
Where an Auxiliary Control is located on a class design then the Executive officer is present there instead for the purposes of damage calculation.
I would also like to see a 3 Ton (0. 03?? HS) component for FAC / Fighters that represents the cockpit of these crafts. (3 Tons to balance out the 2 Ton Crew Quarters, Fighter
I would further propose that the class design doesn't have a default control rating of 1 but instead zero, and only after adding these systems can it rise, Bridge / Cockpit 0 > 1. Auxiliary Control 1 > 2. And so on.
Making it possible for ships to be unable to carry out orders without a Bridge / Cockpit or an Auxiliary Control when the Bridge has been damaged.
Having all of the control stations being able to be affected by microwave lasers, enabling a mission kill of the intact ship.
I too will also miss the Staff Component of Task Forces, but am more excited about the possibility of seeing my own bridge crews work first.
EDIT: A Tactical officer could then provide the ability for missiles and beams to target specific components of a ship, with an accuracy bonus related to his tactical skill. Allowing really well trained / experienced tactical officers the ability to target a ships engines with 70% accuracy on an observed class, and 90% accuracy on a known class (Thinking about alien ships, you could probably tell where the engines were generally versus ships you have reverse engineered / or salvaged wrecks of as some examples)