Good stuff. Starting from the bottom, the initiative sink issue--this is force building, which has a different balance from battle value. If force building rules required both sides to have equal units, then as long as the battle value is fairly calculated it wont matter. My issue is that a 17 battle value unit exists, but if that unit does nothing other then exist it really doesn't have a battle value, and if both sides are equal then one 17bv unit counters the other and no initiative sink issue exists. I digress.
For me, weapon BV seems best balanced around 5 turns. If it was 10, the value chosen in alpha strike, it could also work, but existing BV cost structures, like one shot weapons, are valued at 20%, so 5 turns is the value chosen by TPTB. 5 turns is also enough to really change the game state in normal btech played on 2 paper maps--games going for 30+ turns on 3x3 maps id argue are not ones we can ever find balance in, as the scope is too different from the core gameplay. When you do your rolling 5 turn damage spread, heat is much better balanced, as is ammo. Ammo past 5 shots per gun doesn't cost extra BV, to help the ammo versus energy discrepancy. IE, the mech with 56 shots of gauss ammo for 2 guns isn't being forced to pay an arm and a leg for 46 of the 56 shots, like it is now. Heat, instead of doing +6 per turn which is obviously not sustainable, is now +6 over 6 turns. This provides the necessary difference units like the Spider 7m, with 16 heat generation and 10 dissipation, and the 8m, with 16 generation and 20 dissipation, deserve. Currently they cost the same, which is obviously off. Also, heat should be calculated as the best BV/heat, not the highest BV first. Currently, the Rifleman pays for the 2 large lasers first, and the AC/5s are half cost. In reality, the AC/5s are always fired first as they are more efficient per heat, then 1 large laser, and everything after that would be discounted. Weapons on a grossly overheating mech that never get fired in a 5 turn rolling average should be discounted down to 20%, which represents that 1 in 5 turn alpha strike. In the rifleman example, the AC/5s and 1 large laser pay full value, one medium laser will pay 40% value for firing 2 times (for the 6 floating heat the calculation allows), and the second large laser and medium laser will cost 20%, being weapons of last resort that never actually fire, but do provide some value to have in a pinch. 20% is plenty fair.
I agree with you, as pulse is undervalued, BUT... mathy stuff. A PPC, stock standard, is 176. That same weapon with -2 from a 'pulse' bonus would cost 233, 32% more. If all weapons were calculated with +3 base to hits, the base of a PPC would be 72 (before adjustments) compared to 141 for a weapon with only +1 base to hit. Thus, in your system using a +3 'guessed' TMM/whatever, pulse would DOUBLE, (+96% in this example), the cost of a weapon like a PPC. On the table, this would mean 9s versus 7s (+110%), and 8s versus 6s (+73%) would be the 'break point' when pulses become better--i dont see many weapons landing at 9s in a normal game such that we need to penalize pulse. This is probably too high, when for +40% for the whole mech, you can get -2 from a better gunnery in the system. On something like a Battle Cobra, 1487, the pulse lasers will go from 265 (at +28% markup with pulse from 207 base) to 378 from a +83% increase. The equal new mech would cost 1859 in your system if the weapons were normalized, versus ~1325 if the guns didnt have the pulse bonus. At ~1325, a 40% increase from the whole mech would make it cost 1855--meaning pulse lasers in a system with a +3 TMM factored into the weapons would make pulse lasers more expensive then non pulse with the WHOLE MECH upgraded in gunnery skill.
Thats a lot of math, but more or less it just shows that +3 calculated 'TMM', while it might seem was realistic and maybe too low, is actually too much and isnt good for balance. The BV change in weapons it would make would mean that you would get really, really cheap long range bracket value with an effective discount, since the +3 would make the value added from, say, an ER PPC's long range of 15 to 23, worth nothing to buy (4 base, 4 range, +3 assumed tmm, means the value purchased from the 9 hexes at 15-23 would be 1/12th the damage, from the 3/36 chance your formula provides with that +3 bonus. AKA, an ER PPC that stops at 14 would cost only 11.25 BV less. Those 9 extra hexes costing only 11 BV is criminally cheap. Id pay 11.5 BV to extend the long range of any gun in the game 9 hexes. Yes, you might be shooting at +3 tmm some of the time, but not all of the time. And when you arnt shooting at +3 tmm, your BV system means that long range weapons will turn anything to dust with less then a +3 bonus, as they get so many more long range weapons for the same BV. Hyperbole, yes, im exagerating for effect. But if you make them pay as if long range is an 11 to hit, and its actually less then that, the value goes from 1 in 12 up to 15/36 for no TMM, a 500% increase, from the long range BV you paid for.