"Ignoring the erroneous assumption that the sole
goal of the tournament is to win games, does this
system have any inherent unfairnesses in it that we
didn't spot?"
Yes.
Whatsamatta U. is a
.500 team. They play Brainiac U. on an easy packet and
get thwacked 375-150. Whatsnew U., a .500 team plays
Bovinia State on the same packet and wins
325-30.
Then Whatsamatta plays Bovinia State, who probably
won't win a game this decade, on the hardest packet of
the tournament and win 80-0. Whatsnew U. loses to
Brainiac U. 150-50.
On an average packet,
Whatsamatta beats Whatsnew 200-190.
Whatsamatta sort
of suffers in their ranking against Whastnew solely
because of packet strength, which is variable. This is
why ranking based on whether you won the game is
critical - it's the only case where you are on legitimate
footing against the opposition - if it's a hard packet or
an easy one, you're both competing solely against
each other.