What's the idea behind leaving control of slats and flaps to pilots in autopilot?
The key thing is that not every flight is the same. Sometimes the landing gear is left up for longer for noise abatement, sometimes it goes out earlier if more drag is required. On a non-straight in approach it's sometimes a good idea to extend the gear earlier. If the brakes heat up too much on the taxi before takeoff, the gear may need to be left down for a bit for extra cooling. 

Flaps are a bit different as they are typically set for a certain speed, but the principle still applies. For example if turbulence is encountered which effects the airspeed, having the autopilot moving the flaps the second the flap movement speed is triggered is unhelpful. 

Basically, these are things that require the active judgement of the pilots considering the individual factors of that specific flight. It's impossible to automate all of this satisfactorily even with pre-planning. Even if you could it would further introduce an overreliance on automation for very little gain.