I won't argue 650 vs 700 but will say I am so damn slow I can't tell the difference.

You will have trouble finding someone with a 650 tube on a ride but in a bind you can limp along by stuffing a 700 tube in a 650 wheel. Trust me, I did it when I rode 650s.

650s will limit you on rim replacements or upgrades, they just don't make that many. But they do look more proportional which I find pleasing to the eye and I know I shouldn't care but I am about the looks on the bike.

My 47cm Cannondale Synapse has 700cc wheels and I have not been able to do the toe overlap. If you are going to start cornering mad crazy or riding crits you might be able to but otherwise I agree the issue is overblown. Cannondale and Specialized (I am sure Cervelo with their excellence in engineering) have worked very hard to reduce toe overlap in their smaller frames, I think it is a lot less of a problem than people realize.