The alternative special modules for some ships like Styx, Sword S, and Reaper take an unbearable amount of time and effort to gain parts for. There should be a way to more consistently gain parts for them, or their part requirements should be much much much less. A 60 part module can easily take over 2 months to get, and that is only if you do EVERY SINGLE MISSION EVERY DAY which takes ages anyways. They should be much easier to obtain and should be less exclusive. Using the ship you wish to gain a special module for should also render a guarunteed part after any battle you play/win. This way it would give more incentive to actually use them during the grind. There should also be default variants to the special modules like there used to be in the good old days. These modules should simply require 5 parts or so, as they are essentially default modules.
With this, Secret Project ships should also get a special module rework or even have some more modules added to select from. The selection should also be just like the current alternative module selection, and not require a hella costly refit to change. This should also apply to destroyers.
If those missions wont require specific activity on specific game mode, it would be easier. Defend captain and deal damage to captain mission is cancer, you feel like mocked when game refuse to give you combat recon after 5-6 tries. I was doing one mission 3 days because of that once. Still got like 3/4 of Mantis module.