It's a common misconception to imagine that manual skills are practiced much in the sim. With all the "boxes to tick" during a typical OPC/LPC scenario and emergencies thrown in, there isn't actually a great deal of time left to practice basic handling skills
I am lucky that my outfit, while practicing flight data monitoring, encourages us to hand fly whenever possible (and advisable). OK, so as freight dogs we have no PAX to upset, but that means we take full advantage of that fact to fly the approach with A/P off/in raw data, do visual approaches, or fly the SID manually, etc. The bottom line is that many of my colleagues, along with excellent aircraft technical knowledge, are also aces at stick and rudder, "seat of the pants" flying. As a (relatively) recent joiner, I feel that there is little we couldn't handle.
Cheers