I've not read all of the responses on this topic, but I thought I'd give my opinions anyway.
I have some experience as a pilot (ex UAS, and a PPL), and also work in aviation research. Although not directly involved with the exercise / biomechanics side of things, my work does involve ejection injuries, and g-tolerance.
Ok, so this area relates just to the fast jet pilots, but your physical fitness (I use this term loosely to cover CV fitness, strength etc) can play a big part in these areas.
IMO the RAF fitness test should be at a higher standard. Both for the reasons already mentioned about "what if you get shot down and have to evade the enemy" type situations, but also so that you are more capable of performing your daily role. Flying in a high g environment is tiring, I'm sure many of you would admit that. The onset of this fatigue can be put back a fair way with an increased level of fitness though.
I think the best way to improve the fitness level would be to have a compulsory training regime that pilot should follow. Weight training should be included in this, including back-strength weight training to help support the spine in the event of an ejection. General CV fitness should also play a part to improve the condition of your heart and lungs.
Probably the best way to increase the fitness levels in the RAF would be to put the beer prices up in the mess though.
I see someone mentioned the bleep test. Can anyone tell me what are the actual levels you have to get to on the bleep test to pass the annual fitness test?
As for why different people in different roles do the same fitness test, that is because the bleep test is a fairly good test of CV fitness. It is a "progressive and maximal" test, and as such it is quite easy to perform as you don't have to warm up before, and everyone will be able to get a score on the test because it starts at a low speed. It's not perfect, but I don't think there are many other fitness tests out there that perform the role better.