I think it is a big issue in RTW, as AFAIK, you get +1 attack/ +1 defence per level of experience. So with 9 levels of experience, you can have an uber unit with +9 attack/defence. In PBMs I play, we tend to impose a "no retraining" house rule to avoid this unrealistic effect being exploited.
In M2TW, the benefit of experience has been toned down a lot - the maximum 9 levels only give you +3 attack/defence. Given the wide range in unit stats (and the fact they don't seem to determine combat effectiveness as closely as in RTW), that does not seem such a big deal. Personally, I would not seek to impose it as a house rule in a M2TW PBM - especially given the new limits on how many units can be retrained per turn.
I think you could rationalise such a modest advantage to replacements from the beneficial spillover effects of joining a cadre of veterans who could teach newbies the ropes. For example, I know some have criticised the formation of large elite military corps because they remove such potential cadres of excellent soldiers from line units and so disproportionately lower their overall effectiveness.
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