1993 Notre Dame vs 1993 W. Virginia: #2 ND was 10-1...W.Virginia UNDEFEATED and #7th. WV schedule was slightly tougher.
1994 Colorado State vs. 1994 Oregon: Colorado State was 10-2 and ranked #16.. Oregon was 9-4, ranked #11. Colorado States was much tougher
1995 ND vs East Carolina: BOTH with equally identical 9-4 records with ND having a slightly better record and ending up being ranked #11
1996 WV vs Penn St. BOTH have 11-2 records, Penn State ranked #7, WV ranked #13th. Penn St. had a slightly tougher schedule.
And those are the ones I took the time to search. I am sure I went back or forwards 10 years, you will find plenty of these situations.
By the way, ALL this information was easily found on wiki. My statement was based on bigger named(as I stated in my post by adding USC) school will always have an advantage.