OK, messed around with the RSF ships a little, my thoughts:
Gunships/Frigates still tend to get screwed by missiles when moving forward because none of their flares launch forward. Destroyers and above are in much better shape against missiles because their flares actually launch forward. I'm not entirely sure destroyers are able to survive dedicated missile spam, but I'll need to build a pile of Indiana C's and fight some RSF ships now. It may come down to simply changing around the AI's ship variants to bring better point defense.
RSF ballistic ships eat through a TON of ammo now, without Extended Magazines you look for the high sustained DPS weapons over anything else really. They might need some changes to their weapons to offer lower DPS in exchange for higher sustained DPS.
RSF ballistic ships have a lot of hullmods that you want. Powered Armor, Extended Magazines, Augmented Engines, Targeting Core are all very useful but take a lot of OP if you want them.
If the Moscow was good before, it's an absolute monster now if fit correctly. Flares reduce a lot of the need for sideways point defense, since missiles have a good chance of hitting a flare from the side. You still need a bit, PD rotary guns do the job of shooting at stuff that got past the flare screen. The 42mm Flak cannons shoot a little too far, but are great for handing frontal point defense. Linked beamers (which could probably be replaced with Laser Beams) do the rest of the point defense. The Moscow's main cannons still run out of ammo quickly, but destroy whatever is in front of it. With Powered Armor the Moscow can take a real beating and survive. Its only real downside now is that without combat skills, it maneuvers like a brick.
On another note, if the particles for the Laser Tri-Beam could be brighter, that would be great. Currently, it looks a little wimpy next to a Linked Beamer when the Tri Beam is doing around 4 times the damage, but has roughly the same brightness.