There should be punishment for being routed from the field. If the player has invested 600 MP, which is a hefty amount and difficult to save for in the mid game, he should have the ability to extensively punish routing blobs from the field by bombarding the enemy base. Retreats should be as tactical as your advances, if you've blobbed up your forces and A-moved then had it routed, you deserve to have it hit by the barrage on your base and take the increased MP bleed for it.
I will admit it is annoying as hell when one unit is instawiped while sitting there etc; but I don't feel half as bad when my Sturmtiger is doing the wiping. If my entire army is in one place and gets nailed by a barrage I don't think 'Nerf artillery!'; I realise it was actually pretty poor play by me to have it gathered up in that situation.
You shouldn't need LoS to fire. You've scouted the position and so know what you're shooting at. In terms of range, in 1v1 shooting the base sector should be allowed for reasons above, but it can be extensively annoying.
OKW counterplay is difficult 1v1 as it requires almost definite sacrifice of a tank, or a risky assault followed by a stuka. 2v2 and up it is usually fine, don't complain about trucks being bombed: OKW forward positions should absolutely be allowed to be targeted (where base sectors are often out of reach); it's the price you pay for the shenanigans you get to employ. If I deploy my trucks outside my base sector I am aware that I am opening them up to be easily barraged (and the more forward the truck, the more accurate the barrage on it).
Move around your stuff in the FoW. The luftwaffe didn't forget where London was each night of the blitz and need to recon it first