I hate it when people bring up that Zoro was trained by Mihawk and Sanji had to run from trannies. Sanji was forced to fight the 99 most powerful fighters trained by Ivankov, one of the leaders of Dragon's revolutionaries.
Something that everyone also forgets about those two is that Zoro's goal is to literally become stronger at any chance he gets, whereas Sanji is more of a guy who fights when he has to, so Zoro is pushing himself in battles far more than Sanji. Add that Zoro is the first mate and Sanji 'only' the cook and it pretty much explains why Zoro's bounty and reputation are higher when they are equals in strength.