I've seen a comment from Second Measure somewhere (Can't find it right now) that the phased mission approach being used in Atlas and Mercy isn't going to replace traditional missions. Rather, it's being used at lower levels to take a lot of strain off the servers. Levels 1-10 and 50 have a major percentage of instances being generated, and the later has a lot more teams. A collection of phased missions at low levels apparently make things much less stressful on the server. Spawn rates are still being tested... And I'm not sure what they'll do about the crowded cave problem.
EDIT: Aha, found it. http://boards.cityofheroe...=3795329&postcount=5
EDIT: Aha, found it. http://boards.cityofheroe...=3795329&postcount=5