Actually I think the story (and the game in general, such as police chases and free roam) are so much better on free-aim. Not only free aim but default (non-DLC) guns also, too. So no rocket launchers, no grenade launchers, very limited grenade use, and no using the excessively powered DLC assault rifles from the start of the game.Its because the damn story mode is built around auto aim. I hope Rockstar fine tunes their shooting and doesn't build around auto aim next time.
I got my butt kicked a lot even on auto-aim the 1st time I played the game but after beating it a few times, I find the missions (and shootouts in general) so much more fun on manual aim and just using SMGs/basic assault rifles. Auto-aim or r/g launchers make it so easy once you get used to the controls. The biggest thing is just getting used to the movement/cover controls and learning to not run-and-gun (live and die by cover). When cops got shotguns or NOOSE got SMGs, you die so fast outside cover but if you place safe with cover, game is balanced well (and super fun) on manual aim with just rifles.