Simple concept really. It would be good if it was possible to retrain troops. It would allow for more complex strategy and I do not think there are any real negative side effects to allowing this. It might require a bit more programming but it's hard to see it being that difficult to implement.
Basically, it would be good if you could reconfigure troop traits (and equipment) at a cost of production. You could "send" your unit to the barracks or whatever, in which case it disappears from the map for x amount of turns (depending on the costs of the traits you want to exchange for), then comes out after x turns reconfigured as desired.
It seems silly at the moment that you can't, once you have researched the right technology, to at least equip your troops with the armors and weapons your faction has learnt to make.
It is not much of a step further to allow trait reconfiguration at the same time either.
All in all, this would encourage early game units as you know you can prevent them becoming obsolete later on.