I think I have solved it today! I will put it in Word and send it to you so you can play-test it. Small Formations (2-12 bombers, 1-2 flights, maybe also three flights 16-18 ships, haven't decided yet) will be used in the MTO and PTO. I think you could combine it with low-level mission rules too (which I must revise completely).
It will be a bit difficult to find your bombers for the enemy, but once found, there may be intensive fighter attacks. Does it make sense? Before enemy contact you have -2 on MT-2. If you have encountered enemy fighters or flak you have +1 on MT-2 next turn. If there is no contact, the next turn is again -2.
You have an option of deciding how your formation will be. Will you decide to fly in formation or in a loose echelon? If loose, you may fly evasive action, as if you are out of formation, but if in formation you will use the Fighter Pilot Status modifiers.
Fighters will always make successive attacks and if you roll 51-66 for a fighter (which will be removed) during the last wave you must roll on MT-2 again.
This could work... I will put it together and try it and then send it to you.
If this works... the MTO expansion can be play-tested (excluding sea sweeps).