I vote keyed ignition and a column shifter.
This is a no brainer to me. Trucks are about functionality. A column shifter is more functional as it frees up so much centre console space, plus it's likely cheaper to build. Also, I like to rest my hand on the shifter to adjust the radio while I'm driving.
As for the key versus the push to start...I personally couldn't care less for push to start. I've had it in a couple of cars and it's honestly pointless. One time I dropped my wife off and she left the vehicle with the fob in her pocket. 30 seconds down the road the car started alerting me that the key had left the vehicle. Great "convenience" feature that made me have to turn around to go get the fob. I'd rather have a mechanical system that works along side a digital security feature. Add an immobilizer along with the key and that's fine with me.