If I had to pick between Paul and Johnson I'd actually prefer Johnson to run and Paul sit it out. Partially because Ron Paul is getting a bit old, let's face it, and he deserves some rest in his age, and even more because Johnson doesn't have the baggage with Republican voters the way Paul does.
Unfortunately, voters often will never, never, never admit they were wrong about someone else being right. They'll turn on a candidate like Obama, loving him one minute then hating him the next, but it's extremely rare that they start out hating someone and then swallow their pride and admit that "he was right and I was wrong." Gary Johnson can talk about the same issues Ron talks about (and he has) and people won't instinctively dismiss him, which is what I'm afraid will happen to Dr. Paul.
That being said, I don't see at all why they can't both run. I know people say they'll split each other's vote, but there's a lot of campaigning that goes on even before votes started getting cast, and I think it's infinitely more important that our movement be able to say, "Look, perspective! Ron Paul isn't the only one saying these things! It's not just four people in their mothers' basements!"
After all, it's a lot easier to paint someone as "fringe" if not even one other candidate agrees with what he's saying. Like the war issue in 2008, when basically everyone in America could plainly see that the War in Iraq was a total failure, Dr. Paul was the one who looked "out of touch" when confronted with 8 or 9 other people who were ACTUALLY out of touch but in agreement with each other.
Gary Johnson can at least be someone who forces Republicans to admit that there's a real diversity of solutions in the Republican Party to our country's problems, not just a diversity of candidates all selling the same thing.