I’ll get more into the ‘ride review’ in part 2 of this article, but I honestly prefer the feel of 650c, now that I’ve ridden both.
Are you sure it’s not just the longer front center you prefer?? Or, perhaps some other geometry feature you changed from your normal steed? 
I don’t know… impossible to say. I controlled for everything we could, but it wasn’t possible to have everything 100% identical. Even if I kept the chainstay length exactly the same between bikes… perhaps that isn’t appropriate and I should really do chainstay length as a percentage of each wheel size… or something like that. >shrug<
I know for certain that the key contact points are the same. Also - same saddle, pedals, crank length, etc. It’s wheel base, front/center, and that stuff that ain’t to-the-millimeter. All I know is that I really like how the bike handles. I got back on my 700c bike today and it just feels different… I feel like I’m riding much higher off the ground, and I’m not.
Now this is starting to sound like the 26er vs. 29er MTB debates :-/
I know, right?! I hate to say it 
Honestly, however, the ‘feel’ difference is not something that is make-or-break for me. I don’t have a ton of miles on the 650 bike yet, either. It took me a few rides just to dial the position to the final mm. In the end, I’m going to ride 700c, because that’s what my personal bikes have - the Serotta is going back at the end of the year. It was just fun to do an experiment. This did show me, however, that 1) I like a longer front/center than I previously thought, 2) A little more trail doesn’t hurt and 3) I’ll err on the lower side for bb drop. I’m one of those guys that doesn’t need a custom bike, but I love the process of dialing everything in.
I do think there is something to the ‘feel’ of different wheel sizes. There are just a lot of cooks in the kitchen. Overall weight, rotating weight, wheel base, front/center, center of gravity, and so on. In my experience, the smaller wheels (and everything else that goes with it) seems to result in a more ‘fun’ feeling bike. And - it makes fitting easier for a larger portion of the bell curve.