As I have already shown, the game uses two different formulas for experience loss, depending on the type of the unit (land or air). However, only one replacement rate can be set to an HQ. Is this a problem? I think the answer should be a definite "yes".
In the (simpler) case of ground units, taking replacements always increases the combat value. If we can ignore the eventual bonuses for certain experience levels (of which the naming of Soviet Guards units is the only one I'm aware of), it is always good for a unit to receive replacements. From this point of view, the Soviets in 1941, for instance, should set their replacement rate everywhere close to 100%. The Germans might consider a more careful distribution of their comparatively scarce replacements; but, in critical spots, they should also aim for a high rate (they also have "favoured" units, which train replacements quickly).
But the situation is totally different for air wings. Units with high numbers of aircraft seem to take higher losses (!). That means they'll need more replacements; because they lose just as much XP as the less populated ones through this process, the net result is that large air units lose experience quicker than small ones. Also, smaller groups of fighters seem to fight more efficiently, i.e. lose fewer planes for each enemy shot down, so they should gain experience quicker. Now, XP has a very important role in the air: for instance, it is checked and, if it should prove too low, the wing might participate in a mission at half strength or not at all. Taking all these into consideration, the air units are better off small and experienced than large and ineffective (take the I-16, for example: it has better ratings than the Finnish Mixed Fighters and fights in much larger numbers; yet, because of its lack of experience, it is cut to pieces when set against them). Therefore, the WiR player should aim for quite low replacement rates for air units.
So here is the dilemma: I'd like to set replacements to 90% for land units and only 30% for air units (this one gives me groups of 50-60 planes, which are just fine). But I can't, because they are in the same HQ! I can't assign them to different HQ's: the aviation would no longer support the ground troops during the combat phase. So I wonder: how could Manstein or Jukov solve this type of problem when it occured to them?
My suggestion is this: the land troops are rather OK; so, either change the (highly unrealistic) XP loss system for air units, or - make them take replacements only when set on training.

"Power always thinks it has a great soul and vast views beyond the comprehension of the weak" - John Adams