I've noticed the same think. Mine's an '06. This is the clunkiest transmission I've experienced (I've owned 3 other bikes). The shift from 1 to 2 is the worst.
Maybe it gets better with different oil.
Usually the tender will come with a small harness that you can attach to the battery. Then you run the harness somewhere accessable so you don't have to 'take the bike apart' to get to the battery every time.
After an absence from bikes, I'm back in the game. My wife wanted me to get rid of the bike when we had a kid... but it was always in my blood. I decided to ease back into it so I picked up an '06 fz6 with 700k on it.
So far I'm liking the bike but I think I may miss the liter twin I used...