On other forums there have been lots of complains about the new SB 900, special with problems of overheating and the fact that it has maybe less power than the SB 800. The cost is also higher.
Anyway I have the SB 900 and have yet to get it to overheat, and you could turn of that feature. I would also think that if you had a SB 800 and SB 900 shooting side by side they would both get hot at the same rate, but the SB 800 would not warn you of overheating.
That being said should Nikon sell the SB 800 again as maybe the SB 800 classic