I would like to see the FCS defined at the level of one ship of cruiser size and up along with its associated support vessels - destroyers, light cruisers, etc. Including cruisers is useful because smaller powers may not be able to afford dreadnoguhts and you can have an interesting campaign without them. IMO, a squadron of 6-8 cruisers should be able to take on a solitary battleship, albeit with losses. Plus it gives more strategic options. Battle Riders would be independent along with their Battle Tenders. A fleet carrier would be assumed to have its fighter's abilities factored into its various ratings. Squadrons of like types would be reserved for things like merchant ships. Scouts really should be relegated to the background, IMO.
Using the sector map is the obvious choice, but each system potentially has multiple interesting areas to attack and defend. When the interest is merely passing through, you could pick any gas giant to refuel from at a minimum, and there may be other planets or belts that could be used. Certainly the mainworld is the most important spot, but defending an entire system can be challenging, depending on its configuration. A larger hex could be used and each defensible location could have its own location. Imperium used a half parsec hex scale to support this. Freedom in the Galaxy and The Sword and the Stars also have similar ideas. There could be also be off-map boxes for each hex, similar to what is done in FFW.
I would like to see SDB combat handled with a different combat system than fleet combat. It is more analogous to sub vs. surface than a wet navy surface combat.
Maybe I'm too old school, but counters seem like the right format for this level of game vs. miniatures. I suppose either would work - if this is a general system, the factors probably have to be recorded on a side record.
Possible factors:
Cost (RU)
Time to build (units depend on final scale)
Attack - FFW had an overall attack factor. Could split into long range attack vs. short range attack factors. Could differentiate by type of armament with a letter code corresponding to the Traveller5 weapon letter. Imperium split out missile and beam factors.
Defense - FFW has defense, Imperium has screens. Some form of defense factor is needed no matter what. Could differentiate active defenses from passive ones or screens vs. armor.
Movement - FFW ships have a jump number, which is the most obvious one. TCS also has a refueling code - whether you need that or not mostly depends on scale. Maneuver and agility are both potentially useful in addition.
Sensors - Both sensor and stealth ratings could be incorporated.
Tech level - Ideally tech level is factored directly into the factors. Better tech -> better factors.
Flavor - special equipment could be noted with special codes on the counter. Probably don't want more than 2-3 of these at the very most. I'm thinking of things like Black Globe generators - stuff that adds capabilities beyond a standard ship of that class.
There should be a way to go from FCS->BCS and vice versa. The RU used should translate into credits (accounting for maybe half the credits going to supporting vessels) and the requirements to get the factors needed should be clear. Evaluating a ship design to get its FCS factors should also be straightforward.
I would rather see a combat resolution system like TCS that adds up factors and works out a result than a system like Imperium where dice are rolled for each ship.
I like the scale of FFW (1 week per turn) better than imperium (2 years per turn) in some ways, but I could also see designing a system flexible enough to be used at either scale, or at some intermediate scale. 2 weeks per turn makes sense, but you could imagine other scales like monthly, quarterly or whatever.
I like the campaign rules of TCS in principle, but they are probably too hard to deal with in practice. FFW plotted movement is a nice way to address communications lag. Longer scale turns also help with this.
I'd like to see economic development addressed if the scale is longer term like Imperium. Should be able to invest in colonies, build and upgrade starports, etc.
I see this scale of game as supporting role-playing primarily by providing the background for more local stories (ala FFW), but it would be nice to also address various ways that players can directly influence the course of a campaign. A good GM can just make it up of course, but it's always nice to provide examples.
All of this should be easily translatable to my own custom Traveller universe, disconnected from the OTU.