I like the boss idea, but the problem with that would be the same as with Flash events timing and some people wouldn't even be able to take part in it, so it would need a bit of thinking. I really like the idea, nonetheless.
What about sending a digimon on a mission? You wouldn't be able to use it in your team. You could have different energy, skill or type requirements and get different rewards depending on those. This way, people would use the digis they don't usually use in their teams and look forward to different skills and digimon.