Here's how it breaks down for me (as an owner of Roku 3 and ATV 3):
Roku advantages:
Extensive app store and some very cool private chanels
Auto-bookmarking - start where you left off for almost every app
Headphone jack in the remote (huge for nighttime watchers with sleeping family members)
Cross-app voice search
User Interface - not great, but better than ATV
Media playback options (local media, DLNA, cast support, etc.)
ATV advantages:
AirPlay support
Results may vary:
ATV uses a different content delivery network, so streaming quality could be better or worse depending on your internet provider and their peering agreements.