Currently, we have the ability to subsidise civilians and to seize civilian ships (in a somewhat flawed manner). Unless we get a nuanced tax system that adds depth on its own, with more colony-bound civilian activity, it probably won't add much.
And now for something completely different: The missile will always get through. That's a bit of an elephant in he living room, especially when trying to have solid evolving doctrines in a multiple-faction game. Less so in a game against the AI, because of the non-competitive nature of the game.
What I find strange is point-blank missile fire ignoring non-CIWS defence gets removed: That quirk adds depth and flavour, and is probably good for variety & balance. More powerful and less risky methods aren't touched even when other changes will increase the problems:
1) Multiple missile variants moving at the same speed are in multiple salvos when fired from one fire control. Emulating frequent Soviet practice of firing 2 almost identical missiles with different sensors gets this effect, even if we don't set out to exploit this by researching the same missile 20 times. There are of course other legit ways to have multiple variant of the same performance - e.g. different agility/warhead/fuel splits.
2a) One missile per fire control is the natural state for fighters in the style of a torpedo bomber. This is not a problem currently, but may be in the future with the changes to sensors (sensor fighters will detect larger sensor ships earlier than vice versa, making small fighters very difficult to intercept).
2b) Short-ranged missile fire controls that just aim to outrange beams are tiny and dirt cheap, again allowing an easy split into many salvos and limiting defensive beams strictly by fire control. Without the constraints (short range, high speed to outrange larger beams) of point-blank fire. Again, the change in the sensor model makes this much more effective.
3) A launching platform exactly as fast as the missile is very difficult to defend against (tested this with a 1000t FAC firing a clump of 91 size-1 missiles in 91 salvos. Scaling this up and using two-stage missiles gets rid of the extreme speed requirement for the launching platform). If this is deemed problematic, we could get a tech line for how many salvos underway a MFC can handle. OTOH, slow missiles may be easy prey to a very fast beam interceptor in area defence mode.