Yesterday I was on 1201 from LAS to ORD and 1201 from ORD to EWR. I was able to check-in on line, though I was not given the option for mobile boarding passes. No matter how many times I tried, the app said checked-in, but gave the option to email the passes for printing.
In July I had no problems using the mobile boarding passes for all but a partner flight. I usually get the paper passes anyway, because I would hate to be "that guy" holding up the line because my iPhone is acting up.