I also have bikes with both 700's and 650's - I prefer the 700's. I don't find them aesthetically displeasing at all.....

Tubes - no problems finding 650 tubes, but then again I do live in the big city and have tons of shops to pick from. 650 long stem tubes for my deep V's are a little harder, but still not impossible. If you have to rely on chain stores you probably won't find much.

Tires - definitely less of a selection. My 650 wheel bike is my commuter and getting hold of good puncture proof winter tires was a bit difficult. They always are a special order and many models are not available at all. I had Kendas that I really liked, but they stopped making the 650 size and I went with Gatorskins, that I don't like as much, when I replaced them.

Rims - the selection actually is kind of sucky.... Yeah you can get high end tri wheels, and they are often cheaper than the same in a 700, (this came in handy for outfitting my TT bike, which is also 650) but try looking for a more heavy duty rim. Like I said my 650 bike is my commuter/winter bike. I found the selection of nice sturdy rims to be sadly lacking

As far as the cons of 700's

I don't find my 700 wheel bike to be odd looking or disproportionate
I don't find the handling of my 700 wheel bike to be twitchy or even any different from that of my 650 bike
I don't have any toe overlap.... (though I will admit to having very small feet)