I agree. The '06 may have gotten the frame and suspension upgrades in anticipation of the new engine. The handling differences are probably slight, and in a race between the two it would probably come down to the better rider.
The new engine is quite different performance-wise, though... (I said different, not better!) The '07 motor is heavily oriented towards torque and power in the low RPM's, whereas the tried and true Gixxer motor is a high-rev horsepower mill. When you ride one you'll notice the difference immediately.
As far as the engine weight, I'm not sure which is heavier, or by how much. The exhaust on the '07 is responsible for most of the weight increase. How it affects handling will remain to be seen when/if I change the muffler.
I dunno... this bike is so quiet it's spooky. I think I like the "stealth factor", being able to sneak through small towns without attracting attention is a nice feature.