So far, the major difficulty in Fortress Mode is the fact that farming may or may not be bugged: dirt and sand that's underground has to be mud before you can farm there. Some mud's naturally occurring, but most of the stuff you'll excavate near the surface isn't. There's also some question about whether seeds are being listed as unavailable when you actually have some with you.
I abandoned my first fort after growing impatient with my solitary miner, who wouldn't mine more than one tile at a time without taking a break in her room and then in the dining room and then back in her room. Maybe I needed to have a doctor look at her or something, but her thoughts and feelings didn't indicate any sort of unhappiness or injury; she just decided she wanted to spend most of her time standing around with No Job listed as her current task.
