@Cinth
Wait it can use railclusters? I will have to check my game later. (Cant right now) Either I didn't get railclusters or it bugged out and wouldn't let me put them on. I understand that I can't get every mod and its probably only my completionist nature that makes that annoying. Still one thing that is off about that is that one of the traditional spire weapons is the Heavy Beam Cannon. And the Spire Hull cant use that either. Then there is the fact that missiles out dps both photon lances (probably shouldn't given the weakpoints of lances) AND plasma siege cannons (what is this, i dont even) against even large targets like the nebula bases. (aren't siege cannons supposed to be better at nuking the big things than everything else?) Now factor in that the siege cannons cant hit smaller targets (or did that get changed and I missed it?) and things seem rather unfair for the Spire hull.
Yep, railclusters are a large mod split between Spire and Zenith hulls. The module is a little stronger than the fleetship with the same bonuses. HBC are a FS weapon but the FS don't have lances they can equip. Plasma Siege mods have the same bonus damage as the equivalent MK Plasma Siege SS. Plasma mods should be able to hit the ships in scenarios (so bonus damage against the heavy hulls) since they aren't fleet ships (I'll have to play test this one to be sure). Lances could probably stand to get the reduced cycle time like the main guns do (for the same reason).
Right now the best ship to clear out nebula bases with is the Zenith, (going off the numbers and personal usage) and that doesn't seem to fit right to me. The human gets the most light slots, and seems to be best at dealing with the largest variety of smaller things. The Spire has the most large slots, but the two (possibly 3, but railclusters are more a small target thing) mods it can use don't have the best DPS against such targets. One would expect that the Zenith hull would be in-between those two. (Nienzul doesn't really rate in this, but it does other things that none of the others can, so its ok)
Problem goes back to the issue of weaponry. Since missile mods have the best dps, and Zenith can mount the most of them, it naturally does better than the Spire, despite the fact that the Spire hull gets more heavy slots. I feel the ratio is right for light:heavy (4:1 or 3:1 if I recall) so that doesn't seem to be an issue imo. Nor do I feel that the dps of the missile mod itself is the issue. More that the lances and siege cannons aren't doing enough. Possible suggestion; Bring the base dps of the siege cannons up by a large chunk. (Not sure on numbers right now) and drop the bonus multipliers slightly. For the lances just up the dps. I don't see any reason that missile mods should out dps either lances or siege cannons. (I'm alright on missiles out ranging them)
It seems the biggest complaint is the inequity in damage dealing between heavy modules, namely missiles vs lances and PS.
So lets take a look at the bonus damage and see where it is. I'm going to use MK V modules (using my current game and I have MK V mods).
Missile Module MK V : 625,000 DPS ((500,000*5)/4)
Plasma Siege MK V: 500,000 DPS ((400,000*10)/8)
Photon Lance MK V: 377,143 DPS (2,640,000/7) *2 second duration, 5 second reload so damage is over 7 seconds total*
So the missile mod clearly outclasses its peers. Giving the Photon Lance the reduced reload will help it out a lot and make it rather competitive. The only way to make the direct damage between missiles and plasma is to make the base damage the same across all marks. This would either be a buff to plasma or a nerf to missiles. In this case, I think it would be reasonable to just buff the plasma since it gets the x10 bonus instead of a flat out high base damage (would limit how OP the plasma could be outside). The MK I change in base damage isn't that great either (MK I plasma would go up by 20,000 damage for base damage). That would put the bonus damage equal to that of missiles.