I don't much like Reload Factor myself (as I've said before). I would much rather just track ammo. But it is part of the rule system, at least for now.
How about making it where weapons do different damage based on shots fired? But reduce the average damage per bullet when more shots are fired? This would be for TW Battlemech-scale combat, not for infantry-scale combat.
So using an assault rifle as an example:
you get the most damage per bullet when firing single shot, and the trooper has the lightest ammo load
you get the most damage per turn when firing in full-auto mode, but you have to carry a lot of ammo
3-shot burst provides an average between the two
Using the following numbers as examples (i.e. not actual numbers, just to show the hypothetical difference)
Single shot: does 1 pt of damage per turn (the shooter can take extra time to aim properly)
Triple-shot: does 1.5 damage per turn (some careful aiming, the second and third rounds are likely to miss)
10-round full-auto: 3-4 pts damage per turn (spray & pray, not all rounds will hit, and not all will hit the right spot, but there is still a lot of shots going down range)
Assuming clips store 30 bullets, and you want 60 turns of infantry fire*:
Single shot: carry the assault rifle and 2 clips
Triple shot: carry the assault rifle and 6 clips
10-round full auto: carry the assault rifle and 20 clips
Carrying more clips will mean less available kilogrammage for carrying other stuff (i.e. better body armor, better sensors, infantry TAG, etc)
* turns of infantry fire would be part of the Infantry platoon construction rules, where whichever main weapon is selected for the platoon, you take the value '60', multiply that by the ammunition consumption rate, then divide that by the magazine/clip/battery/flask capacity, round up, and that is how many magazine/clip/battery/flask each infantryman needs to carry. So if they are armed with pistols having clips carrying 11 shots each, and want to use single-shot, that is 60 * 1 / 11 = 60 / 11 = 6 clips. If they had wanted to double-tap, that would be 11 clips of ammo. This value of '60' can be changed to whatever TPTB decide is appropriate. I figured it was a good value for an infantry unit able to fight 2 battles of 30 turns each, firing each turn.
For weapons that need multiple turns to reload (i.e. muskets), they would technically fire at a slower rate (2-3 rounds per minute), you could set the whole unit as firing at the same time, or take an average for the damage. So if the musket unit took 3 turns to reload and did .3 damage per musket, then each musket could be treated as doing .1 damage. Or you could set the musket unit as needing 2 turns of not firing before it can fire again, but each musket would do .3 damage. Switching freely between the two during a BT-scale battle or tracking individual reload times would not be recommended. (actual numbers will vary, I just wanted to make the math easy)