Actually there are alot of different ways in which the player could signal the game that it's time to reload a clip or two; everything from Pip-boy to definable action key. I don't think this would be a limiting factor.
What I think does make adding magazines hard is that there is very little benefit to the player Other than realism, which isn't enough to get most features into modern games. The feature needs to be fun, or have a direct or in-direct fun outcome for it to exist. Otherwise it's just more hardship on the player, and as we have seen the game studios are not keen on adding features that make it harder (look at hardcoe more, which to FWE players of Fo3 sounds alot like kindergarden mode).
The problem with magazines are that they can prevent you from shooting your gun (even if you have bullets in your inventory), as when you run out of loaded clips you would have to switch to another weapon. (I really can't see them adding a reload-clip-during-battle option, it would be ridiculous to even try). Also the magazines would add alot more complexity to how much ammo you have Available to shoot with, and from my experience thats a pretty big jump from "You have X bullets to shoot", which is how most gamers expect guns to work. If we have to buy clips, load clips and deal with all the hardships that reloading can cause with Real guns, the Fun factor evaporates and I can just imagine the game makers turning away from such a concept.
Adding ammunition types and weapon mod kits all has a Fun element to it - find new ammos, trying differences between ammos, modding weapons every which way - all of that contributes to the Game. Reloading with magazine dependencies, while realistic, I think goes farther than Obsidian would be willing to reach.
