Advice on an upgrade.

I am considering upgrading to a 600 or 650 coming from a 300cc, my budget is around $5000. I've been riding for about 2000 miles on a 300cc and I'm getting very comfortable. I love the power and it's perfect however I use the bike to commute and it cannot deal with the highway. I don't feel safe going at a slower speed on the highways as I live in Massachusetts where drivers suck. I am currently looking for a bike for the next season and I want to know what is better of the 600s from Japan. But a side of me wants just to get a 1000cc like a r1 instead as I like the Yamaha brand. I was considering an r6 but with my local prices, it's about $500-1000 more than the 600s. What are your thoughts?