I'm using a naked domain. The biggest reason why I'm using it is because my domain name as minimalistic as it can get (six characters long, seven if you count the dot) and I sure as hell love saying to people to just type in my alias and add .me at the end.
Although I did not know about these issues, I have to say that the source really didn't give me strong enough arguments to convince me to go through the hassle of making the switch.
With that being said, I opened up a couple of links from the source and I will look through them and see if they'll change my mind.