Is it the Honda 750 or the Yamaha 650 that you're considering? The title of the thread is different from your post. You've got $6000 to spend? My advice is to buy a used bike. You're already on a Harley oriented forum and after you've ridden awhile, you most likely want a bigger HD. If you blow the $6000 on a new metric, expect to lose half that money when you sell it to move up. If it were me, I'd look for a used, low mileage, 2004 or 2005 HD Sportster. If you buy it right, you won't lose any money on resale. They're nice bikes and you can probaby buy a used one with some nice upgrades included.
The Honda and the Yamaha are both good bikes for everyday commuting and some short highway trips. I've spent some time on the Honda. Neither one are as comfy on long trips as a bigger bike would be. Even on day-long rides, you'll want a bigger bike.
Without a doubt someone will chime in and say they own one and they ride it all day... well, I used to own 800cc metrics too, and I also rode them all day. The difference is night and day between those bikes and my FXDWG. After a couple of hours on the metric, I was looking for a place to take a break and I felt beat at the end of the day. After a couple of hours on the big twin, I have to stop for gas and I can't wait to get back on it. At the end of the day, I am sad to see the sun go down. That's the difference...so no matter what you buy, keep resale value in mind... cause you'll be selling it before long.