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I agree about the EOS 650/620 cameras. This was an entirely new system without backwards compatibility for the most part (though Canon did make a little-known adapter to allow use of FD super-tele lenses). If you wanted to stay with Canon, you had to totally reinvest. In hindsight, switching to an all electronic mount was a very gutsy foreword looking move by Canon. The EOS-M is a little bit like this, being the first 'new' interchangeable lens system from Canon since the EF mount (I don't think EF-S qualifies as such). I suspect current EF lenses adapted to it will never perform amazingly (for AF) and will be large, but at least the electronic mount allows some compatibility. The photography market is more diversified now across more format segments and the EOS-M is not a wholesale disruptive change.
As for Canon in the last decade, I would definitely say the 1DIII. Its problems and the 'coincidental' release of the D3 that it hastily preempted caused a lot of former Nikon users to switch back, and I'm sure, also a lot of Canon users, reversing a lot of the momentum Canon built with the 1D/1Ds and Mark II versions. I still have the two I bought, and when they were my primary cameras, they were at Canon for servicing more often than any other camera I've owned. Though I had many problems with them, I also really liked them when they worked, which was most of the time, excluding bright sun, hot weather sports photography. I think it's only now with the 1DX that Canon has somewhat recovered face and regained the confidence of high profile users in the sports/news market by making a clean break from the 45-point AF design and proving that the new 6-point system is a real improvement.