Here is my list of wants for any new counters:
All ships redone on quality thick board as found in other boxed wargames.
The ship pictures should be high quality, possibly top-down shots of the catalog models.
Circular counters with weapon arc lines or pips. Also turning pips. The circular shape is nice for turns, especially with turning pips as you can just spin the piece to the correct facing(don't forget you need a front pip too, voice of experience making my own bases :roll

Also, the same peg circle in the middle.
Standardized base sizes for priority levels, e.g. 25mm for Priority, 30mm for skirmish, 50mm for raid/battle, and 60mm for War/Armageddon
Fighters would be hexes of the same size as the fighter-flight model bases.
Enough counters for big battles, e.g. 20 of each Patrol, 16 of each skirmish, etc. Yes this is a lot of counters, but I wuold suggest that these be offered by fleet, e.g. you would buy a Centauri counter set.
Fleet-specific freighters, transports, space stations, and breaching pods