screwtype (talking about the cost of retraining here), you do know that the mercs are all set to have a specific cost at specific places. Merc hoplite in Sparta are more expensive than those in southern Italy, but not by much actually (950 compared to 850 I think) and they are quite superior in experience (3 to 0). Go change the costs if you want.
RTR might actually have changed to many things that the game now treats retraining a bit differently, go and check the unit file and see if upgrades are more expensive for isntance. But so far it sounds rather positive that you get expensive but experienced recruits, so the mod might actually have made a good feature by accident.
Anyway, I'm pretty certain I see no real costdifference in a less modded game. We need a tiebraker here (essentially I'm saying that the game gives experienced troops for free and screwtype says you pay a lot for them, right?). Who's up for it?
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