Prime Chuck was an excellent fighter and a true champion, and is pretty high on the list of all time greats, but his status as a legend taints people's views of him when they look back.
Prime Chuck lost to Randy and Rampage. Both excellent fighters, sure, but the idea that Chuck could beat Jones just doesn't jive with me.
Jones is a better, more evolved martial artist. He can beat Chuck a hundred ways, Chuck can only win one way. That's called a puncher's chance. I think Chuck's puncher's chance is better than damn near anyone's, but a puncher's chance is a puncher's chance.
I don't think one is tough to call at all. That said, out of all the styles a guy facing Jones could have, Chuck's is pretty damn good. Doesn't seem like anyone will take Jones down and win. Doesn't seem like anyone will clinch him and beat him on the inside. The only ones who can touch him it seems are guys who can throw accurate hard punches. But I'd rather have Gustafsson's reach and straight punches than Chuck's power and loopy punches. Still, not a bad style to have against Jon, but Chuck just wouldn't be enough.