I have to agree with Torsten: I'd write the thesis directly in LaTeX,only because of the power of AUCTeX and RefTeX (and preview, if youhave lots of plots and math).
For me, org-mode's power overwhelms what auctex brings to the show.
Not having to worry about any \begins etc not only keeps the text
cleaner, it helps me in my continuing battle against RSI!
However, I do agree that reftex is particularly useful and I do miss
some aspects of it.
The preview aspects will of course depend on the topic of the thesis!
Thomas S. Dye, Ph.D.
T. S. Dye & Colleagues, Archaeologists, Inc.
Phone: (808) 529-0866 Fax: (808) 529-0884