It's probably a moot point, as go daddy refuses to put cpanel on fedora 7 anymore, but is there a quantitiative difference for CentOS? Why would go daddy bail on Fedora?
Well, you know the boss rules, right? 1. The boss is always right. 2. When the boss is wrong, see rule #1.
I use CentOS on my VPS. Fedora and CentOS have very close ties, so I doubt you'll have many problems with the move if you do stay with GoDaddy. I'm not aware of the politics or technical issues behind the move, but CentOS is a great choice for a server operating system. I actually chose it after experimenting with several other OSes, and found it had the lowest memory footprint.