I think militarized subsystems is pretty great as is.
For logistics ships, it switches between two different logistics costs, and gives you some free burn if you aren't taking Bulk Transport. I think Bulk Transport kind of delegitimizes Militarized Subsystems because it's the skill you take on your way to the two yellow combat skills, but I still use it often enough. Also you should consider that not the entire game is spent at 240 DP, and I personally am fine with losing 1% damage to be at a higher burn.
For combat ships, it's an OP tax that gives you some flux and leadership skills for losing OP. I've used combat ships with and without militarized, and as of now, I think it's a bit underwhelming on combat ships in most situations, since the skills that you get to benefit from aren't all that impressive. The flux is also nice, since it can get you from being overfluxed to neutral. I use it on remnant hunting atlases.
What I think is the coolest part of Militarized for combat is the two exclusive hullmods. I wish these were buffed to be actually usable, although it might make them a bit oppressive on the ships that are already good at combat like the Prometheus MkII. I don't even think it needs to be particularly viable. Just maybe stuffing a colossus' cargo with ablative armor, and throwing it in combat where it can soak a couple hits in the early game sounds fun, or maybe fitting a kite with a PD conversion that turns it into a usable PD escort.