Good to hear it's coming along nicely.
Even though I'm the one making requests for anti-shield/anti-armor energy weapons. Please please make sure it's not going overboard than its ballistic counterpart. There was this heated discussion in Alex's 0.9.5 patch note on the same matter and various people also make good agreements and arguments about it. I also don't want it to outshine the energy damage type.
Thanks! And as far as weapons go, I *think* I caught some if not all of that discussion in the patch notes thread. In this case, it's partly about different design goals. A lot more ships have combination weapon mounts like synergy and composite, etc in the mod. This is especially true for midline ships. So ship balance is *less* reliant on weapon type - though not completely un-reliant if that makes sense.
That being said, I feel like each weapon type is still fairly unique in terms of both playstyle choice and functionality. For instance, most short range missiles are now flux free, but they are also heavily if not completely mitigated, while short range ballistics are flux free but almost always specialized. Flux free energy weapons, on the other hand, deal higher dps than ballistics (about 1/3 more over the ballistic equivalent) and have a faster projectile that is harder to dodge, but have less range. Less range is fine though, because most ships that would use them have speed advantages. In that way it's similar to vanilla design. Energy damage weapons seem to favor the energy weapon type if only because of the higher dps. The Heavy Photon Cannon has 100 less range, 20% less armor penetration, and a lack of burst damage over the Eclipse Cannon in return for less OP and double the flux efficiency. On paper the Heavy Photon Cannon has slightly higher dps, but the burst damage element of the Eclipse Cannon (especially when considering exp magazines) realistically causes the weapon to perform better in comparison from what I've seen. For any easy guestimate if the burst dps is 669 and the sustained is 200 I'd put the actual dps at around 300-350 -ish in most situations. That is compared to the 229ps of the Heavy Photon Cannon.
The new weapons are more intended to fill non-existent niches rather than overlap with ballistic counterparts. The Terrabane Cannon is not really competitive with ballistics because at 0.4 flux efficiency it generates significantly higher flux than the flux-free Heavy Dual Autocannon for only a very tiny bit of extra range and higher overall armor penetration. Dps is the same between the two and the Terrabane has worse accuracy. If it were a universal or synergy mount, I'd more often than not take the ballistic weapon for most builds so I could utilize my flux elsewhere. The Graviton Driver is slightly less clear cut and I'm keeping an eye on it. It has more dps but half the armor penetration and less burst damage compared to its closest competitor: the Hypervelocity Driver. It is a lot more efficient but has less range and a higher OP cost. The main reason for it is that energy weapons completely lacked an anti-shield projectile weapon at the medium and large levels. Since there were less fire support weapons as well - other than beams with adv optics of course - it seemed to make sense to go that route. From tests, I think the Hypervelocity Driver is better at its role, but I will say I'm less confident of that than I am with the Terrabane Cannon and its competitor.
Re: Armored Weapon Mounts
Yeah it was
amazingly good with larger heavily armored ships like the Onslaught and Legion. (It stacked with the percentage bonus of the faction hullmods to net even more armor on those!) And it was complete garbage for small low armor ships like the Wolf. Now it should have a place in more builds. The extra 100% additional health to weapons is a sort of consolation prize to heavy armor ships (who have a lot more armor on the small end now). Its cost is the same as it was, so it is very cheap compared to something like Heavy Armor or even Automated Repair Unit - which would serve a similar purpose without the armor bonus.
Re: Advanced Optics
Hmm, ok let's discuss some details and see if that changes opinions. I'm definitely open to suggestions, but beams are super tricky both because of their accuracy and soft flux generation causing a two-pronged balance conundrum.
Pics for easy stat comparisons:
A bunch of pics of in-action effectiveness and flux build up on a midline light cruiser:
And finally, a battle between a Strike Paragon and Elite Onslaught - one using basic strike beams and one using adv optics:
Ok, so right off the bat you can see the dps difference between the beam and the artillery as well as the much poorer flux efficiency of the artillery compared to the pre-adv optics beam. This is because the unmodified beam is a strike weapon. The Enforcer has 1700 armor and the beam does a good job of penetrating through despite the very high armor rating for a destroyer. When adding adv optics, however, the beam now has 1300 or 1500 range depending on the beam - but! - becomes as flux inefficient as the artillery. That is the intended design goal.
When you combine those stats with the fact that the beam is crazy accurate and doesn't do something like max the Aegis' flux meter even with that kind of range on it, I think it skews to the beam's favor despite the nerf to adv optics. This is especially true when fighting off fast and maneuverable ships like frigates. Sure, the artillery is a little more damaging to the armor itself overall (when it hits) and the extra OP saved from not needing the hullmod helps overall flux efficiency for the build, but I wouldn't call the beam combo bad by any means. (It does help that most beam-using ships will have good flux stats and typically a larger OP pool to begin with.) Part of the reason for that is the accuracy as I stated, and part of the reason is the higher dps since the beam starts as a strike weapon.
Now for assault beams like the Graviton Beam, they get the added benefit of being surprisingly competent PD weapons and assault weapons to start off. Their flux efficiency is very high but there
is a small flux cost considering their dual role and effectiveness. Add adv optics to the build and once again the role changes - from assault to heavy assault in this case. Since the PD role is maintained, I think it is a pretty interesting concept to have a very long range PD weapon that passes through (and almost always destroys) any missiles in its path but is still an effective heavy assault damage dealer. The downside of its very good performance is the now higher flux generation that makes the weapon similar to any other heavy assault weapon (like the Railgun). Since flux costs are a larger part of the equation, it is unlikely that the build can support a bunch of strike or fire support weapons alongside it without serious flux stats. However, that also gives missiles like the Reaper, Atropos or Heavy Annihilator a chance to shine since none of those weapons cost flux yet remain viable strike weapons. (Keep in mind not all stats are final as testing is still occurring.)
As far as the suggestions for alternative balancing mechanisms, technically I don't think I can distinguish between assault and other kinds of weapons because it is not in the MutableShipStatsAPI so it has to be between PD and non-PD beams. I've tried damage reduction before and it doesn't seem to work out very well. From what I remember, it mostly slows down the battle if the opposing ship is low tech because it loses armor penetration but keeps the shield up enough to allow a lot of kiting. I'm not completely sure if there is an API for recharge time - which might be better than pure damage - but I have a hunch that if there was I would have used it before switching to flux costs.
That is the thought process behind the changes at least and testing is promising so far as the pic demonstration kind of shows. Granted that battles have a fair amount of random variance and that's why I have to track trends, but the two builds were very close in performance and the "Fire Support" adv optics build actually was a bit worse off as intended. Now keeping the two large side-facing weapons as Atronarch Beams? That would likely cause the Paragon to lose to the Onslaught as that would be more of a "Dedicated Fire Support" build... but watch out smaller ships!

Any thoughts/concerns now that the details are laid out? Hopefully that explains the reasoning at the very least.
*EDIT*
Well, I have tested a few weapons out extensively tonight since it came up. For now, I am going to remove any flux costs from the Graviton Beam and Graviton Lance. I'm not convinced all PD Assault Beams need zero-flux yet, but the particular weapons I am changing are kind of weird because they are balanced around
kinetic soft flux. This is fine when firing at a hullsize lower than a cruiser since the dps of either weapon usually outpaces dissipation and has a visible impact to the flux battle. Armor penetration is limited enough that it doesn't feel more powerful than something like a Twin Tactical Beam when you consider the different weapon roles. Where it really gets sour is when facing high tech ships at the capital level with a large dissipation value. It seems to do very little in comparison to hard flux options (part of the reason I created the Graviton Driver in the first place) or even just zero-flux or projectile assault weapons. For this reason, the added flux is hurtful enough in that scenario to make it completely unviable - and advanced optics hurts rather than helps because firing at missiles can build flux up too fast in exchange for very little noticeable impact to the overall ship-ship flux battle.
For that reason, I am going with zero-flux and hoping that the OP investment for advanced optics will be enough to make 200 additional range on either weapon a consideration rather than a no-brainer. If that feels too strong at the small ship level considering the weapons' zero-flux perfect accuracy with fairly high dps for the weapon class, I may go with basileus' suggestion and remove all benefit to PD weapons while simultaneously removing all of their flux costs across the board. Or I'll reduce the range bonus to 100 instead of 200, etc, if that feels better.