One thing I feel needs to be pointed out in this thread is that Militarized Subsystems may act as a noob trap. I might be the only idiot, but in my early runs I used to pick it for the Burn increase and the Sensor buffs, not realizing that I made civilian ships eat into my fleetwide buffs with their DP despite never using them in combat. Doesn't help that Insulated Engine Assembly seems strictly inferior at first glance.
I never really found a good use for Militarized Subsystems in my later runs. True civilian ships plain suck at combat and putting the hullmod on rogue faction rebuilds isn't worth it. The idea of a Daud wannabe scraping up a fleet where auxiliaries play combat support doesn't currently translate into the gameplay in any good way.
Militarized Subsystems only eats into fleetwide buffs if you're already running a 240 DP worth of combat ships, though. It is a perfectly reasonable early game choice, especially when ADF is not available yet. If you only need +1 burn on the ship, do not have Bulk Transport, and your fleet is under 240 DP, then Militarized Subsystems is the optimal choice compared to ADF. Like adding a Buffalo to a destroyer led fleet, or a Dram to a frigate fleet.
You just need to realize when the costs do start becoming meaningful to you, which might not be at 242 DP of combat ships say, since that level of slight reduction in bonuses is not noticeable in a play experience sense. You can see it on the info card but actually being able to tell the difference between a 99% and 100% CR ship based purely on their performance in Detailed Combat Reports is probably impossible given the typical wide variation due to AI decision making.
It's the same with Bulk Transport for some builds which don't go down industry, but plan to spend a story point to respec down the line because you want tier 5 combat, leadership and tech. At which point, how many credits are you actually saving over the duration of the time you have Bulk Transport, and is it worth a story point to you? Some might answer yes, and others might answer no. An extra Dram or Hound over the course of an in game year is what, 10,000-15,000 credits? That sounds like the kind of credits one has to spend to make up for the Bulk Transport difference early game to me. Maybe 100,000-200,000 total over the time you have Bulk Transport before respecing? Is a story point worth 200,000 credits? Early game maybe, late game not at all, at least for me.
Well why would I bother myself with civilian hogs when I can achieve a similar result with customized non-civilian logistics ships, except also getting a passable combat backup?
Again, it's an early game situation where you perhaps simply don't have the option. Although as far as I know, there are no good non-civilian tankers other than the Revenant, and it's pure RNG if you find one while still in the frigate/destroyer stage of the game.
Especially in a world where phase ships exist? If you never get into combat, then sure Militarized Subsystems don't have downsides. But I have two problems with this: First, do you really want to avoid one of the most fun features of this game just to optimize your overworld gameplay? Second, isn't it quite a flavor mismatch when Daud's feat is being shoved into the player's face every other turn of a corner, yet a playstyle emulating it is unfun and suboptimal in practice?
I mean, I doubt many experienced players would like it, but one way to make Militarized Subsystems clearly more useful to more players to is to prevent the ability to skip the limited selection of ships and hullmods phase of the game. I believe in the current game there are many players who simply do some black market trading to build up a pile of credits to buy a perfect fleet, or at least the starting core of one, and then proceed into actually playing other phases of the game, such as combat or exploration.
One way to change that, is to make civilian ships, and civilian adjacent ships (combat freighters such as the Hound, Cereberus, and Mule) be the only ones that can be purchased off the open market, and also the only ones that can be purchased off the black market without high pirate relationship (similar to how military markets restrict combat ship purchases based on relationship). Similarly, lock all new hullmods behind faction markets (and skill picks, which then makes the various skills which provide hullmods much more important). This then requires the player to do something more than trade to build up credits. They need higher relationships with factions, to gain access to better ships. This interesting has a side effect of making black market trading more painful (due to the negative relationship that happens from it), as faction relationship becomes critical to being able to outfit a fleet as you want.
Alternatively, entering combat with inferior (dare I say militarized?) ships becomes more attractive, as it becomes a direct shortcut to specialized combat ships via salvage. Similarly, colonies and exploration becomes a third option to bypass high faction standing, although on a longer timescale. Hitting up bars becomes more important as coming across a surplus combat ship being sold via contact is rare and valuable opportunity.
Which means potentially risking combat in sub-optimal ships in order to build up that relationship, or at best, frigates purchased off the lowest tier of faction military markets. Alternatively, by going directly to combat with sub-optimal ships, salvaging becomes much more important as it becomes a short cut to specialized combat ships without the reputational needs.
In such a drastic change, I'd make the faction military markets even better stocked, so that once you've unlocked the reputational tier needed, it becomes relatively trivial to get the faction related ships and hullmods you want, and probably weapons as well. And on the other hand, you wouldn't see combat ships in the other markets at all, except for high pirate relationship in the black market. Pirate relationship becomes your "street cred" in that case.
Unless the game changes such that people are forced to play through the early phases of the game like they play through the end phases of the game, Militarized Subsystems is always going to be considered underpowered by the players skipping that phase. The entire concept of it is incompatible with perfect end game fleets, simply because it is a "make do with what you have" hullmod. If you're never just "making do" with a limited selection of options, the hullmod is never going to look appealing or make sense to you. I'm not sure if such a drastic change would be overall better or worse for the game as whole, but that's what you're going to need to do if you want to see anything along the lines of militarized subsystems be useful to the majority of players.
On the flipside, does Venture without Militarized hullmod count toward skill DP limits? Because that's actually a competent combat ship. By current logic, it should not.
Venture without militarized subsystems neither benefits from nor counts against skills with combat ship limits.