Well, I know what the first s-mod I'm building in for the early game flagship is. I'll take a +25% damage bonus against nearly the entire enemy fleet.
Anyways, the way I view this, and the better deserved s-mods, is not a change of the original hullmods, but rather introducing an entirely new set of hullmods that have a different resource cost (s-mod slots instead of OP). Especially when you provide bonuses that you simply cannot duplicate with OP. That are not allowed to stack in the same way Integrated Targeting Unit and Dedicated Targeting Core are not allowed to stack. Those unique bonuses are going to cause competition with hullmods that do not provide additional benefits, irregardless of the OP differences.
I also tend to like to look at how things impact the entire build, as opposed to taking things in isolation. Which leads to me want to rephrase the penalties some of these new s-mod hullmods are getting as a bonus for the OP costing hullmods instead.
So I'm wondering, is a +100% or it sounds like potentially now just an increased +50% missile rate of fire worth 5 DP on a cruiser or capital? That kind of DPS difference is like a capstone combat skill all in itself. Those are some pretty big DPS increases for pretty cheap, for otherwise identically fit ships. I mean, compare to the Graviton beam's +5% to shield effect. For less than the price of a Graviton beam, I can get 50% more flux free missile pressure, as long as they last compared to the other ship. Sounds like this more traditional OP costing hullmod is a much, much better deal than this new s-mod slot costing hullmod. My question is, how much of a missile DPS buff should 5 OP buy you on a capital or cruiser. Given most damage buffs are pretty small shifts, like the +10% for Scattered Amplifier, or +5-10% from the Graviton beams, or the +10% from Ballistic Mastery. I feel like spending 5 OP should at most buy you that much on a capital, not 50%. Even the 15 DP difference from the advanced turret gyro presented here is a mere 25% against certain targets.
Unless the ships have a small missile loadout (i.e. Paragon), I don't see how such large differences in DPS could be balanced between similar fits. Personally, I think a 10% shift in DPS (so more like -10% instead of -33%) would be more in line with the what the rest of the game numbers typically look like for DPS differences between identical ships with different hull mods. Assuming you keep the disadvantage at all. Depending on the uniqueness of these new s-mod slot hullmod bonuses, it's possible the OP savings won't be worth it relative to some other benefits.
The +25% maneuverability buff for the traditional OP Heavy Armor compared to the s-mod slot Heavy Armor is at least in the ballpark, given 15 OP is about 60% of a the Auxilliary Thrusters hullmod OP cost on a capital, which is a +50% bonus.
On a side note, if you're looking to nerf missiles overall, then applying a rate of fire penalty to both the OP costing expanded missile racks and the s-mod slot version would make more sense than just the s-mod version, perhaps with an OP cost decrease. At which point EMR becomes more of a tradeoff hullmod like Unstable Injector. More speed and less range. While EMR would be more sustain, less DPS (although more overall damage in the long run, but less good at bursting down shields/armor).