Here's a question I've been pondering: given a ship that has some number of hybrid (or universal) slots, what stat modifiers does the ship need to have in order for energy weapons to be generally competitive with (but not overshadow) ballistic weapons? ("Generally" is an important term, here; it's not hard to find niches where one specific energy weapon, for one specific purpose, can compete with ballistics. But if you have a ship with a bunch of hybrid slots and no stat modifiers, most of them should be filled with ballistic weapons.)
Edit: To clarify, this post is aimed at "How do I make a modded ship with large numbers of hybrid slots both balanced against vanilla ships -and- have both energy and ballistic weapons be generally useful in those hybrid slots?", and is explicitly not a suggestion for any sweeping changes to actual base stats of vanilla weaponry.
My thoughts, so far:
We can either buff energy weapons or nerf ballistic weapons; which way to go probably depends on the base hull's stats. A fast ship built along generally high-tech design parameters would need to nerf ballistics in order to fit into vanilla balance; a slow hulking vessel built more along low-tech lines would need to buff energy weapons (in much the same way that the Onslaught's TPCs are long-ranged and flux-efficient).
Range is the most important stat to balance, followed by flux-efficiency.
In the buff-energy-weapons case, a simple +200 range should do nicely; that puts small energy weapon range at 700, medium at 800, and large at 900, roughly on par with typical ballistic weapons range. (And also puts beams up to 1200 range, which matches the Gauss Cannon; on the assumption that this case applies to vessels that are built along low-tech lines, that kind of range is probably okay.)
- Side-comment: I'm pretty sure the flat bonus applies after percentage bonuses like ITU. If so, then we'll need to make that flat bonus vary based on presence/absence of ITU or DTC, increasing the flat bonus by the appropriate percent. Should be doable.
Nerfing ballistic range is rather touchier, given the larger variance in ranges and the existence of extreme cases; a simple reversal of the energy weapon bonus (so -200 range) would give seriously out-of-gamut results like 50 range vulcans and 800 range HVDs/Maulers. I'm not sure if there necessarily is a good general-case solution. The best I've got at the moment is -30% & +50; it's -not- a perfect fix, but it doesn't penalize short-range ballistics too badly, gets average-range ballistics down to roughly comparable with similar energy weapons, and doesn't let the long-range outliers have too much of an advantage (750 range for an HVD, 890 for a Gauss Cannon, versus normal medium energy range of 600 or large energy range of 700.)
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Which brings us to flux-efficiency. This one's complicated by two factors; one is the judgement call of "how much do we need to adjust this?", and the other is the available variety of ways in which the issue can be addressed; you can alter the flux-efficiency of a weapon by modifying damage, or flux generation, or (arguably, depending on whether or not you assume the ship is mounting its maximum number of flux vents) even ordnance point cost.
The judgement call part of it is complicated; in the ideal case you'd have one high-per-shot-damage weapon to break armor, with the rest of your arsenal devoted to weapons that put out high DPS versus shields; DPS versus hull is a distant third priority (especially now that there's no hull regen skill). Ballistic weapons, with their varying damage types (HE vs. Kinetic) play perfectly into this ideal case.
Looking at medium weapons, you've got at one extreme the Heavy Needler, putting out 420 DPS against shields for a mere 170 FPS (but with a mostly-ignorable 25 armor penetration strength), and the Heavy Mauler with an armor penetration strength of 400 for 225 FPS (but only 50 DPS versus shields).
By contrast, energy weaponry offers the Pulse Laser with 100 armor penetration and 300 DPS, at cost of 333 FPS, and the Heavy Blaster with 500 DPS, 500 armor penetration, at the cost of 720 FPS.
This means that, for breaching armor, one Heavy Mauler is roughly comparable to four Pulse Lasers (the exact math gets complicated due to armor's nonlinear scaling; this is a -very- approximate congruency). Four Pulse Lasers is 1200 DPS vs shields; one Mauler and three Needlers is 1370 DPS vs shields - conveniently about the same. Flux costs, though... the Pulse Lasers run you 1333 FPS, while the Mauler+Needlers runs at 735 FPS. On the other hand, Maulers and Needlers also cost more ordnance points than pulse lasers; the 17 OP you save by swapping to Pulse Lasers could (in theory, if you're not capped out on vents already) dissipate 170 FPS; if we factor that in, then the Pulse Lasers are behind by ~400FPS.
This suggests that if we are buffing energy weapons, they should get a roughly 33% reduction in flux costs, and if we're nerfing ballistics, they should get about a 50% increase in flux costs. That's probably too much, though, as the energy weapons have one additional hard-to-quantify advantage: the advantage of versatility. If you only have one or two medium ballistic slots to work with, you can't get as much of an edge out of the ballistic weapons' specialization, while if you have one energy slot, it's exactly 1/4 as useful as four energy slots. Let's try -20% (energy buff) or +25% (ballistic nerf) and see how well those numbers apply to more extreme cases...
And hey look, we've got a great extreme case in the Heavy Blaster; this singular weapon deals 500DPS versus shields, and has 500 armor penetration strength, meaning that -one- heavy blaster is, all on its own, stronger than two slots spent on a Heavy Needler + Heavy Mauler combo. A heavy blaster costs 12 OP, and runs at 720 FPS; the Needler+Mauler costs 27 OP and runs at 395 FPS. Assuming we can spend the difference (15 OP) on vents again, that puts the Heavy Blaster behind by an effective 175 FPS... and ahead by an empty medium weapon slot. If we apply the flux cost adjustment we calculated as being reasonable for the Pulse Laser, then our one Heavy Blaster is only behind by ~35 FPS (for the -20% energy weapon flux case), or ~75 FPS (for the +25% ballistic flux cost case) - and is still ahead by one entire weapon slot. Not good. And worse still, if we're dealing in hybrid slots, we have to consider the case where the player mounts one heavy blaster and fills the rest of the slots with needlers...
Conclusion: if you've got medium hybrid slots, and you've balanced for range, you can't give more than about a 10% flux-generation edge to energy weapons, thanks to the Heavy Blaster being kindof absurd. It's likely that similar calculations will work out for large slots, because Plasma Cannon. That said, if you -don't- balance for range, it wouldn't be hard to justify the original -33% energy weapon flux cost or +50% ballistic flux cost suggested by the Pulse Laser calculations.
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TLDR: My current best hypotheses (not yet tested in game, this is all theorycraft at this point):
For a slow, low-tech styled ship, energy weapons get +200 range and -10% flux cost. Or energy weapons get -33% flux costs, but no range boost.
For a fast, high-tech styled ship, ballistic weapons get -30% +50 range and +25% flux cost.
Things still to do: I need to make a mod that lets me test these numbers in-game, modifying vanilla hulls of high-tech and low-tech ships to use hybrid slots & have the appropriate above adjustments.