Wow...that's unbelievable. Not sure how a pilot is going to remain proficient at raw-data if they never do it. I don't see much point in flying cruise portions (with people walking the cabin, and only needing to hold altitude and heading) but flying a descent or climb is good for keeping your brain sharp. Maybe I'm misinformed, since I fly a turboprop with no AP, but I thought we were certified to fly an aircraft through all phases of flight within ATP (or, at the very least, Commercial) standards.
Smurf, my best advice is to keep teaching your students the same way, but add in a little more about the G1000, even if it comes during the prep for the stage check. If the student is good and prepared, it shouldn't be a problem for him or her to pick up the glass system stuff. After all, there's no substitute for a good, basic foundation of skills. You may only have to show them once.