The heroes seemed to think it extremely unusual and dangerous in ST5:TFF to try and fly in a shuttlecraft non-automatically and without tractor beam guidance. If the beam is an essential aid at the late stages of approach, that is, at the bay doors, it's probably also precise enough to juggle the shuttles inside the bay and the hangars, in the TOS movie era already.
But then again, the tractor beam seen in TNG "Time Squared" was a rather visible and obtrusive piece of equipment. If shuttle juggling were routinely conducted by those, wouldn't the shuttlebays look different?
Using the shuttles' own hovering machinery, perhaps under complete computer control (that is, the computer of the E-D operates the computer of the shuttle Joyride directly, without the need of a humanoid-in-the-loop), sounds simple enough. But it might be argued that powering a shuttle up and down for mere shuffling purposes is hard on the hardware. We never really see a shuttle being precision-maneuvered under its own power after landing anyway, and certainly not outside shuttlebays and hangars.
This leaves room for ideas about small "tug" 'bots or clamp-on antigravs or tractor beam pistols or the like. They would be the cheaper or safer way of achieving what the shuttles and ships certainly could do all by themselves.
Timo Saloniemi