Hi hazed!

The reason why you got that many points is that Ju 88 is regarded as worst bomber to survive and and cause damage, ENY value is 40 (same as bf 109F-4 or other fighter plane that is rarely used) and OBJ value is 25 which is same as for any fighter and higher than any other bomber, for example lancaster has OBJ of 10.
Bombing barrack (factory) gives you nice points because you can kill several targets with single heavy bomb but it is an axception. Attack to any other factory does not give more than 15 points in Ju 88, even if you land. Believe me, I have flown Ju 88 lots this tour!
So, in Ju 88, usually 15 points for landed mission from factory, max 35 if target was barracks. Is this unreasonable when compared to other bombers? I don't know.
But I do know that Ju 88 has lowest K/D ratio of all bombers because of its small size and ineffective defensive armament. If you are attacked you are pretty much dead, I have been attacked some 5 - 7 times and everytime I have been killed without single kill caused.
If you compare the points gained by bombing factory to sinking a CV or even destroyer they are ridiculously high. TBM survival rate is very small and if the attack succeeds and, say, CV gets sunk it should provide truckload of points. Lets think about actual navies, how many CV's did Royal Navy have in beginning of war? I think something like 10. Then how many factories large there were in britain? Many! So killing CV is more important than damaging a factory which could be rebuilt.
Killing CV's (and capturing fields) should be rewarded much better! I think rewarding pilots who flies extremely rare and difficult to survive in bomber like Ju 88 rather than some 4 engined monster is ok like it is now.
These things will be surely adjusted, our job is to give feedback for those adjustments.
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