The main argument to be made for Pre was the number of American records he owned at one time. Pre had 7 American records. Bob had 3. To be fair, Pre's # of records were a bit inflated as it included 3 miles and 5k, 6 mile and 10k. Bob didn't get a chance to race for the 3 mile and 6 mile records. Pre also had greater success at the NCAA level. He wins the matchup there.
Secondly, Prefontaine fans will point to his competition record, overall, as a leg up on Bob. Yes, 24 1st place finishes from 1968 to 1975 was impressive but there's an elephant in the room. I believe Pre ran against clean runners for the most part (The Finns excluded perhaps). Bob, a clean athlete, was routinely up against known or suspected drug users.
For example:
Mohammed Mourhit,
Ali Saïdi-Sief,
Dieter Baumann,
Brahim Lahlafi
1997 WC 5k final:
Daniel Komen (KEN) 13:07.38
Khalid Boulami (MAR) 13:09.34
Tom Nyariki (KEN) 13:11.09
Ismaïl Sghyr (MAR) 13:17.45
Dieter Baumann (GER) 13:17.64
Bob Kennedy (USA) 13:19.45
1995 WC 5k final:
Ismael Kirui (KEN) 13:16.77
Khalid Boulami (MAR) 13:17.15
Shem Kororia (KEN) 13:17.59
Ismaïl Sghyr (MAR) 13:17.86
Brahim Lahlafi (MAR) 13:18.89
Worku Bikila (ETH) 13:20.12
Bob Kennedy (USA) 13:32.1
There was a strong suspicion that the Moroccans were doping (men and women). They had a national program and a lot of times away from the limelight doing their own thing.
The main case for Bob is that he raced against arguably the greatest distance runners of all time and in an era when the African invasion was so decisive that elite distance running, as a sport, was under real threat to be totally and utterly extinguished from our psyche.
He broke 13 or was close to 13 when it mattered and it was still a big mental barrier. He didn't hide in the comfy confines of Oregon for training post-collegiately. He sought out the best to train with (Daniel Komen) and often traveled intentionally for months for training. Pre's equivalent would have been if he sought out the Finns and other Europeans to train with for 3-4 months at a time. Pre would have never done that as his ego was too big.
Make your case for either Pre or Bob!