I agree with Barry that a good workaround is better than nothing. I have not yet tried the seperate cable trick, but I am getting close to this step. Currently I'm working through a very similar set of problems. I have two MacBook Pro units (13 and 17) both of which suffer the same problem when connected to my Thunderbolt 27 - the TBD does not wake from sleep. For the 17 this occurs about 1 time in 3 and for the 13 it occurs every time.
I recently had my TBD back to Apple for repair who concluded that with both the 13 and 17 displaying the same problem, it could not be a machine issue. Of course it could be a software issue but I decided to go ahead with hardware repair to rule this out. My "repaired" TBD came back and there is no change whatsoever - problem is still there.
Having read this thread through, and others like it, I'm also thinking that virtual machine software could be a problem. The other thing both my 13 and 17 have in common is they both run VMware Fusion all the time.
I shutdown Fusion on the 13 and it works perfectly. I can repeat this every single time: run Fusion and the 13 will not wake the TBD from sleep. Stop Fusion and it wakes it every time. With the 17 the result is the same.
So, there might well be multiple problems here, looking back at the thread, but for me and possibly others, I think VMware or Parallels might be a contributory factor. Now, the question is where is the bug? Something common to both VMWare and Parallels or something lower down within OSX or drivers that is only precipitated when running VM products?
Assuming I'm right I am now looking at workaround solutions (perhaps minimising Fusion before sleep etc) to see if I can find a stop gap solution. I have also reported the bug to vmware and I'll report back here when I find out what they say. I might also try Barry's solution to see if that adds further to the pool of knowledge.