Initial work on Transformers Prime's third season is set to begin in 2012, according to a Twitter post
by series storyboard writer Bryan Baugh: Well, today is my last day at Hasbro Studios... for a few weeks, anyhow. We got a stretch of down-time before work begins on TFP Season 3...
This might not come as a huge surprise as Hasbro's intentions for Transformers Prime are that it becomes a new and ongoing universe. That being said, plans can change.
Please also bear in mind we've not heard that Season 3 has been officially greenlit yet - but the fact some work is being planned for early 2012 certainly suggests that announcement is not far away.