Every final drive system have their pros and cons. Chains are the cheapest, lightest and most easily manipulated (alter gearing). Belts are the most silent and smoothest and clean and need little attention. Shafts does not need regular cleaning, are oblivious to the elements and wheel alignment never change.
On the downside, chains are a little messy and want some lube ever so often, need relatively frequent replacement (typically 15-30k mile intervals), plus rain, snow, salt and dirt will shorten their lives. Belts can pick up a stone that will put a hole in them or even break them, they can squeak badly, altering gearing is difficult and costly at best. Shafts have the most unsprung weight, has the highest friction losses, need partial dismantling to have their splines lubed, and wheel alignment cannot be corrected if off from the factory. And with their V-Star series, Yamaha have proved that they can make a shaftdrive system you can cock-up every time the rear wheel comes off. Altering gearing very costly/difficult and repairs are expensive, but very rarely needed. Unless you have a BMW or a V-Star.
Personally, I still prefer shaft drives, but I would not let the final drive system dictate my choice of bikes.