I recently watched an interesting video of an austrian economy professor, who came to the conclusion that our current competition based society is in effect because in the past competition was crucial to survive, and thus people competed. Our current generation competes because we grew up in a competitive society and in order to be truly cooperative, cooperation needs to become a part of our "memes". Here's the video, unfortunately in German and no subtitles are available yet:
http://www.youtube.com/watch?v=Oouoee9UvEc.
I think the main problem with group bonuses is that those who know/think they worked harder will feel treated unfairly. I have no information on how group bonuses are perceived or what their effects are. However, I personally think that the main problems come from teams who don't share the same spirit/culture and thus, those problems also exist in individually rewarded teams.