Both are fine bikes. Your question would be like asking someone if they should get a Ford 150 or a RAM 1500. All the ford guys are going to say "Oh get the Ford" and all the Dodge guys are going to be "man, you need the RAM, it has power!" and then you'll have the random Chevy guys saying "Silverado 1500, it's the last truck you'll ever need". It's all on how you setup your bike. People might say something handles better than something else but the truth is an 2007 vs 2008 bike stock from the same manufacturer can have dozens changes that make the bike better or worse depending on you. Best for you to look at both bikes, check out what (if any) after market changes have been made, and go from that point. If the Honda and Yamaha are the same price but the Yamaha has a Penske shock (or some other high quality after market shock) and the Honda doesn't you might want to consider the Yamaha. Good luck, I hope whatever you get ends up being an enjoyable ride for you.
They make power different honda more midrange and R6 more top end. I say go with the midrange. You use it more coming out of corners.
Yeah I agree the nice thing about the Honda's is parts fit from other years, but I'm sure the same applies with the R6. I race an '08 600rr and I think it's an awesome bike. I'm not particularly biased toward the Honda it's just what I have raced and have a lot of Honda spare parts. For club racing I do have a lot of spares on hand because a lot of the time i'm the only guy on a 600rr. As far as motor goes in stock form the Yamaha's have the legs. I have a SS motor and it's pretty comparable to a stock R6 motor which I've found out from racing at Willow Springs. I've raced an '03,'06, and now '08 and the '07 Hondas are pretty solid race bikes. With this being said I've never raced an R6 but it would be fun to try one out.