Or just make the set bonuses only active in their respective content, therefor the set gear for that specific bit of content should always be the best option beating out ones from the other bits.
Some members of the playerbase will play an unhealthy amount if you give them the option too, and will complain about it. Really the only thing Blizzard can do is force them to stop, or otherwise segregate the different gear paths to their path alone. Of course this gets rid of any ego those players might get from going around one shotting world stuff, but oh well tough luck.