When you watch airliners' flight videos on Youtube, you see pilots still control the slats, flaps and landing gear during the climb and landing phases even after autopilot is engaged. Why doesn't autopilot simply control them when it is capable of it with help of the FMS? Why is their control still left to pilots, who anyway depend on the FMS (if they have one) to figure out the "right" configurations?
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.
It makes sense to not automate certain flying tasks, because there are two sides to automation:
- On the positive side, it prevents routine mistakes.
- On the negative side, it can create an unnoticed deviation during malfunctions.
There are flight accidents where automation actually was part of the cause of the accident, for instance the Turkish Airlines 1951 mentioned in this question. Also, the automated fuel trim system in this incident tried to fix the imbalance from a fuel leak by automatically transferring fuel from the stabiliser trim tank into the leaky wing tank, of which the flight crew was unaware.
If the pilots set the configuration of the aeroplane, they are physically involved in setting its state - their fingers and brains will retain this information much more readily when needed in case of emergency, than when a system does it unseeingly.