In an article at Variety talking about films getting converted into 3D, the trade says it is still a possibility that Transformers 3 might add a dimension:
Bay's next project is "Transformers 3," and there have been discussions among Bay, Paramount and Industrial Light & Magic about going 3D with the pic. The big stumbling block is the extra time required to do production and visual effects in 3D, as the movie's release date is already set. Having the pic post-converted could alleviate that problem.
The third installment is scheduled for a July 1, 2011 release.