Thunder punch would be better because with that move set there will be the following benefits.
1.) There will be 551 out of 800 Pokemon that blaziken will be able to deliver a super effective blow to.
2.) There will be 249 out of 800 he will only be able to deliver regular damage to BUT.....
3.) There will be no Pokemon that will take "not very effective" damage (1/2) AND
4.) There will not be a single Pokemon that he cannot damage. There will be no "it doesn't affect foe Pokemon".
As long as you know which moves to use and you know your match ups, pick Thunder Punch and all this will be yours.