Thank you for an elaborate reply, you do raise a lot of points in this.
First I'm just going to say that I was manually targeting but it's beside the point because you confirmed that it's not supposed to work atm.
#3
In my opinion fixing #3 would be the best thing you can do right now - and then balance nukes/railguns while taking that feature into account (right now autofiring nukes using momentum is really powerful, making it also targetable will potentially make it op, however it would be really fun to use bombers with nukes, so maybe reduce the explosion range for nukes to compensate?)
Issue #4
To the issue #4 and it's impact on the game: right now the range increase is only useful for fast cannon walls and autofire nukes, I don't think the fact that it happens is a bad thing, however the difference in proj speed and thus lifetime is too great right now.
Personally I absolutely don't like 2nd solution in it's current form because it would really remove fluidity from the game, however partial implementation of this could be interesting (read more ways to balance this)
Projectile speed
In general I would prefer projectiles in this game to be faster, it's just incredibly frustrating that you can outrun bullets with normal engines (maybe make it possible with boost engines?), but I don't think that every projectile needs a buff - there is a threshold I think, of when the projectile becomes too slow to gain the range effectiveness - examples would include nukes, I don't think I'd want them to become faster even if their lifetime gives them a longer range.
More ways to balance this
In general I prefer gameplay solutions to gameplay problems, artificial limitations, while balance things don't feel fun or interesting in any way.
One of the ideas I had is having more use for sensor array in the targeting department - make it increase the weapon targeting range as well, and thus have the second solution partially in this. If you want to have range advantage - use some expensive (and sometimes maybe heavy?) parts. Maybe even add some antennae/dish like external parts that specifically cover a limited angle of where they are pointing to.
PS: also Flak can pretty much render missiles unusable and it's all kinds of weird mechanically, also its fire makes a smokescreen you can't see through, but it's probably a discussion for another topic.
EDIT:
A small idea for balancing the cannon projectile speed increase is making their recoil much greater, making them harder to use on light ships.