I started this thread thinking merging units was standard policy in the series that now had become a little bit less clear cut . Apparently merging units is now a neat trick you can apply but only in certain circumstances. Obviously, I'll have to change my view on the matter as I was unaware of certain mechanics that changed since ETW.

I didn't know you pay a flat upkeep regardless of depletion unlike the previous games (as far as I'm aware of). This does mean that merging 2 units into 1 is a good way to get your economy back in order after a conquest.
I also assumed that the experience was still tracked per soldier. This is a very elegant mechanic that was implemented in the early games and I see no reason why it would be changed. However, if the experience would be tracked per unit, merging would become useless as a way to acquire veteran units.
The last reason for merging still stands. 1 full unit can be more desirable than 2 depleted ones. This is of course dependent on the level of depletion and not always an easy choice.