I wouldn't worry too much about the gearbox . It will smooth out nicely as you get more miles on it . The Mt-09 gearbox is the smoothest Yamaha gearbox I've ever used on par with suzuki gearboxes .To be honest wasn't sure about the colour myself when I first saw it, but the fact it was almost £600 quid less than the black that went a weird purple in daylight (only in my opinion obviously!) swayed it, but now very happy with it.
The gears do feel a bit more 'clunky' then the one I test rode, but hope a few more miles will free things up a bit!