The only time its even debatable that FSU was better than Florida in football was when Zook was there. Even then Zook beat Bowden they year Zook was fired.
Zook was HC at Florida from 2002 to 2004. I would argue Florida State was the better program most of the time from 1987 to 2000 when they finished in the top 5 every single year. Especially when they played for the NC in 1998, won it in 1999, and played in it again in 2000. Was Florida finishing top 5 all 14 of these years?
1987 11–1 2nd Won Fiesta
1988 11–1 3rd Won Sugar
1989 10–2 3rd Won Fiesta
1990 10–2 4th Won Blockbuster
1991 11–2 4th Won Cotton
1992 11–1 2nd ACC champions Won Orange
1993 12–1 1st ACC champions, National champions Won Orange
1994 10–1–1 4th ACC champions Won Sugar
1995 10–2 4th ACC co-champions Won Orange
1996 11–1 3rd ACC champions Lost Sugar
1997 11–1 3rd ACC champions Won Sugar
1998 11–2 3rd ACC co-champions Lost Fiesta
1999 12–0 1st ACC champions, National champions Won Sugar
2000 11–2 5th ACC champions Lost Orange
Now put Florida in the ACC or Free Shoes U in the SEC. How would that look?
OK, well here is Florida's record each year during that time frame:
1987 SEC 6 6
1988 SEC 7 5
1989 SEC 7 5
1990 SEC 9 2
1991 SEC 10 2
1992 SEC 9 4
1993 SEC 11 2
1994 SEC 10 2
1995 SEC 12 1
1996 SEC 12 1
1997 SEC 10 2
1998 SEC 10 2
1999 SEC 9 4
2000 SEC 10 3
And here is the head-to-head record. FSU won 11. Florida won 4. One tie. (16 games played because of two bowl games against each other.) But you don't think it's even debatable that FSU was ever better than Florida other than when Zook was there?

Date Location Winner Score
November 28, 1987 Gainesville, FL FSU 28–14
November 26, 1988 Tallahassee, FL FSU 52–17
December 2, 1989 Gainesville, FL FSU 24–17
December 1, 1990 Tallahassee, FL FSU 45–30
November 30, 1991 Gainesville, FL Florida 14–9
November 28, 1992 Tallahassee, FL FSU 45–24
November 27, 1993 Gainesville, FL FSU 33–21
November 26, 1994 Tallahassee, FL Tie 31–31
January 2, 1995 New Orleans, LA FSU 23–17A
November 25, 1995 Gainesville, FL Florida 35–24
November 28, 1996 Tallahassee, FL FSU 24–21
January 2, 1997 New Orleans, LA Florida 52–20A
November 22, 1997 Gainesville, FL Florida 32–29
November 21, 1998 Tallahassee, FL FSU 23–12
November 20, 1999 Gainesville, FL FSU 30–23
November 18, 2000 Tallahassee, FL FSU 30–7