I remember working with a user batching trees from a long time ago. There is a forum thread hear that talks about batching trees. http://forum.unity3d.com/threads/batching-trees-and-speed-up-rendering.138929/. Much of this applies to Mesh Baker. There is also this page which has some specific info about baking Tree Creator trees with Mesh Baker http://www.digitalopus.ca/site/faqs/tips-for-using-mesh-baker-with-unity-tree-creator-trees/. I think when I tried this before I had to use a shader for the trunk that was not affected by wind and a separate shader for the leaves that was. This is not a perfect solution as the branches don't sway. Unfortunately I believe the default unity bark shader assumes that every tree has its local root at 0,0,0 which is not true for batched trees.