More has been said about the major sources of funding of the effort to pass Proposition 206 than about the substantiative differences between it and 201. Yes on 206 has received a lot of funding from tobacco companies and the vulgar Left, as is their tendency on every issue (just look at what they've been saying about developers and Prop. 207!), has been trying to spin this as a reason to vote against it.
Ours is a free society in which the interests of tobacco companies' shareholders are no less valid than yours and mine. It takes a certain degree of antiliberal audacity, self-interest not being equal to malice, to see malevolence in their fight for the right of consenting adults to use their product in limited settings where others consent by their presence.
In this case their interest happens to overlap with that of bar owners afraid that an outright ban on smoking in their establishments, completely bypassing their property rights, will cause them to lose business.
Proposition 206 isn't the smoking ban we're looking for. It doesn't address sidewalk smoking at all, shifts smoking to patios, and like 201, maintains a presumption that smoking is permitted in the absence of a "no smoking" sign, although it does mandate "smoking permitted" signs for bars allowing such behavior. But in several ways it's an improvement over 201. It preserves the right of bar owners to decide to allow or forbid smoking in their establishments, and doesn't include a gratuitious tax.
Its one drawback is its preemption clause forbidding local governments to further restrict smoking in bars or tobacco shops. Yes, the city of Tempe harmed quite a few of its small businesses by banning smoking, driving bar customers to neighboring cities. Nonetheless, since there are always contingencies, the option to modify the law ought remain open to local governments and abuses fought at that level.
206 is only slightly superior to 201. Given their similarity, it makes sense to vote for both, to avoid seeing each getting, say, 40% of the vote and neither passing.