Speaking as a pilot for a moment, I think your instincts are correct in theory but hard to actually implement.
In a critical function like control, you don't want to split a pilot's attention. You wouldn't want them to sometimes be monitoring a datalink system, but then also sometimes be listening to the radio for deviations. Even if it's less efficient 70% of the time, you reduce cognitive load by training a pilot to ALWAYS go to the radio for clearance and command.
Of course, there are edge cases these days where pilots use datalink for some clearance delivery before taxi and enroute, but you can see how these phases of flight (before you push back and after the auto pilot is on) are selected for very low competing load. In a live terminal environment, you want a pilot focused in one place for instructions.
Furthermore, you're correct that most pilot-controller communication falls largely within tight set of procedures, but deviations are common enough (weather, traffic, emergencies, hold patterns, taxi route, etc) that you find yourself on the radio regularly to sort it.
Last thing: pilots are allowed to say "unable" if they deem an instruction unsafe. I've personally had to do that many times (most common case for me is trying to comply with a vector instruction under VFR with a cloud in my way). VFR may seem like an edge case that commercial planes don't deal with, but again that's not always true in a terminal environment. Plenty of these planes fly visual approaches all the time. And if ATC is talking directly to the computer and not through the pilot, you lose the opportunity for the pilot to quickly and clearly decline an instruction.