First & foremost: Make sure you have comfortable & durable shoes!!
I would consider flat pedals, given all the hike-a-biking, unless you have a pair of shoes you love to hike in for dozens upon dozens of miles.
What are the typical choices for non-clipless shoes for CTR?
I made the switch flat from clipless about a year ago and just cannot imagine going back. I've been riding in Five Ten Freeriders and Evolv Cruzers. Not sure how either would hold up with all the HAB in CTR, and the Cruzers are probably way too minimal anyway.
Anyone know of any durable trail running shoes that would be a nice option for flats?