I have the BoEM in print and the BoEM 2 in pdf. I looked at the CBoEM today at the FGLS and found it to be 50-50. I was already worried that a lot of spells would be gimped after someone posted the revisions to Bolt of Conjuration, but that was the only real change I noticed.
I found the spell section had a ton of stuff I didn't recognize, and magic items too. I figure those are from the BoEM 3, if I recall from flipping thru it the crunchy bits are scattered everywhere.
Things I figured would be changed weren't. Like the Acid spells. In 3.5 Acid Splash, Acid Arrow and Acid Cloud are No save, No resistance spells. The acid spells weren't changed in CBoEM, though I suppose they do some extra things not like the 3.5 acid spells. Further, I expected to see web extras compiled and put into the book, for example
http://www.montecook.com/arch_stuff8.html which I specifically looked for and are absent from the book.
I didn't pay close attention to the monsters, I suspect they may have gotten a better treatment for conversion.
Ultimately, I won't buy it yet cause I can't afford to, but maybe down the road I'd pick it up because I can see the efficiency of having all 3 books in one cover, plus the 3.5 and AU conversions could be useful. I'm not a fan of 3.5, so until I absolutely have to buy it, I wont.