The question is what people will vote for -- the individual characters, or their interaction, or the source material in general.
Phoenix will beat Freeman, np, but I don't see that as a strong rivalry because seriously, who plays PW games? I'm taking Alucard/Dracula over Shepard, who hasn't shown himself to be too strong here, and then to oust Phoenix as well.
On the bottom side, the portal duo will easily beat Ness, but Frog/Magus is going to run the table thanks to the Chrono Trigger connection, and thanks to it being one of the few legit "rivalries" in the tournament.