The primary difference is chemical resistance.

EPDM is good in steam applications and has fair chemical resistance.  It should not be used with solvents or petroleum agents.

Viton has excellent chemical resistance.  There are currently three grades of Viton available:

Viton A - is the most common and should not be used with most Ketones or Esters.  It has varying performance in steam.

Viton GF - is more chemically resistant and offers excellent steam resistance too.  Should not be used with many Ketones or Esters.

Viton ETP - is the most chemically resistant Viton offering the greatest steam resistance and may be used with some Ketones or Esters.

Note:  These are basic compatabilty ranges and should not be used to determine if an elastomer is right for your process.
Before using any elastomer in a process you should verify it's compatability with an elastomer expert.