Eh, Mods are fair. You unlock them to be built permanently, and some mods are extremly good (accelerated metabolism, Tenents of Tranquility, the network controller one if you pick autonom units).
I have more of a problem with weapons and vehicles. Yes, you don't need to pay for them, but in return they are not unlocked. If I want all of my 4 Heroes to wield Malady, I need to pay 1200 renown! I rarely get over 2k renown, so I would have barely renown leftover.
Regarding the unit unlock - you first have to pay 150/250/450 to unlock them as well. You merely have an option to then purchase additional units for half of that. If anything, I would rather like to have the same system for mods, giving the possibility of purchasing a mod to be moved to the arsenal by paying half of the price again.
On a sidenote: I noticed that purchased tactical/strategic operations as well as Mods have their price removed, but that is not the case for purchased doctrines. Is that intended, and if yes, for what reason?