Johnson is an "abolish the Fed" guy.
He's bad on economics in general, being he's supply-sider. He's a "national sales tax" and "stop taxing the rich" guy.
He's a "privatize parts of social security" guy.
He's a "destroy public education" guy.
On MJ legalization, Clinton is just as good. She won't legalize it outright, but she will tell the feds not to interfere with states, and she will reclassify it to Schedule II. Just as it was with gay marriage, all that's necessary for change is for the feds stay out of the way of the states, and that's the Clinton plan. Just look at how abortion turned out when it was decreed by the feds instead of the states.
And on abortion, his record is not good. While he's not out to make it illegal, he thinks it should be treated differently than other healthcare, which is not good.
So, he's clearly inferior to Clinton on those issues, and others, and so I see Clinton as the better candidate. Obviously, nobody has to agree. The point is that it certainly can be argued Johnson is not the best candidate.