Yes, I do want to include something that gives the flavor of "beams vs. missiles," but I'm inclined to think more along the lines of adapting the combat system from the old Avalon Hill classics "War at Sea" (WAS) and "Victory in the Pacific" (VITP). As I said earlier, I also want there to be a difference in the effectiveness of beams vs. missiles.
In HG combat, beams (spinal meson guns) tend to kill or cripple ships outright. If a decent spinal meson gun (factor-E or better) hits and penetrates the defenses, the target is almost certain to be killed or crippled.
However, missiles (and other bay/turret weapons) tend to slowly reduce the firepower of the target by numerous Wpn-1 hits on the Surface Explosions table, but rarely kill their target outright; it can usually fall back to the reserve and then jump away since the drives are almost always untouched (this assumes the commander is smart enough to fall back before Fuel-1 hits drain his tanks too much, either).
So what I'm thinking is that in a battle, the two sides line up their squadrons and exchange fire, pretty much the same way it's done in WAS or VITP. There's a die roll (modified by the skills of the Admirals present, if any) to determine what range the combat is at, missile range (long) or beam range (short). At missile range only missiles (Bombardment rating) can be used, while at beam range the commander can use either rating, as he chooses.
Shooting works pretty much as it does in WAS/VITP: each rating point gets you 1d6 to roll, and every "6" is a hit. However, when using missiles, each "6" rolled gets you only one point of damage, which is applied to/reduces only the target's Attack and Bomb ratings, and when both of those are reduced to zero the target is disarmed, but the squadron's ships are still there and can be repaired. Multiple hits add together, of course. When using beams (the Attack rating) each "6" rolled when rolling to hit gets you 1d6 worth of damage which is applied against all three ratings of the target, and when the Damage rating is exceeded the squadron is destroyed.
So missile combat under these rules would disarm ships but not destroy them, making repair more important (and I'd change TankRons into ServeRons that are mobile repair facilities as well as fuel tankers, to allow forward repairs and make those TankRons really valuable). Beam combat vaporizes ships and is really, really destructive.
Of course, there would also be rules for the reserve (you could use the rules from WAS/VITP without much change), suicide attacks/high intensity attacks, etc, etc.
The practical disadvantage to this combat system is that it might require you to keep track of two kinds of danage to a squadron. Luckily every copy of FFW comes with a set of backprinted (white/black) counters for tracking percentage losses of ground units and planetary defenses. Such counters could easily be used for tracking damage to squadrons as well, using the white side for tracking "missile" damage (reading a "10" counter as "1") while the black side could handle "beam" damage.
And yes, the beam and missile damage to the Attack and Bomb ratings would be cumulative, so a 5-3-8 squadron with 1 point of each kind of damage would have effective ratings of 3-1-7.
