I'd like to see the various optional rules bandied about normalized in cost and published in an 'offical' product. Redundant Sheilds, Odd-Ranged Weapons, 'fixed' screens, Three-Turn Weapons.
Dual-Mode weapons with ammo for one mode.
Some provision for stowage/carriage of craft larger than fighters. FTL Tugs, if you will.
A look at how speed and weapon range interact. Not really an 'add something', but are we sure that Engines 12 and Range 4 is as good as Engines 4 and Range 12?
Some way to shoot down seekers and strikers before they hit your ship, on the turn they hit your ship. CIWS.
(I shudder to say this) Counter-based weapons that do not rely on seekers/strikers/fighters/mines/etc. Some way to build something that works like the Romulan Plasma from "Balance of Terror"
Some way to add more decision points, and encourage use of those decision points. Limited Arc Weapons, Ammunition, and Slow-Firing helps inform fire decisions... but more of this is always good.