Well they should make it so magazines and ammunition as separate items, therefore no matter how many bullets you have, you cannot constantly reload more then the number of magazines your holding. You can only reload your magazines outside of battle, but if you are in battle you can only reload your weapon to how many magazines you have. Plus you know that magazines and effing expensive!
This might work in a game like Final Fantasy X, where battles are random encounters and you can prepare (to an extent) your arsenal and characters, but the idea of the Fallout universe is that anything can happen at any time with no choice but to fight with what you have. If a number of Deathclaws ambushes you in the middle of nowhere, with no one to pass by and lend a hand, you're screwed.
Well, thank God I can reload pretty fast, and OMG MY LAST MAGAZINE FELL ON THE GROUND!!11!11 ZOMG I'M DEAD.
And that's how that would go down for lower level characters. Besides, say that each enemy (Deathclaw) needs an ungodly amount of bullets to cripple a limb so you can run away. If you exhaust almost all of your magazine doing just that, and are being closed in by another enemy (Deathclaw) what then? It's just too inconvenient.