As a villain Crocodile > Doflamingo, even as a Croc fan you had to root against him in Alabasta, that's how twisted he was.
Doflamingo also had that good backstory which Crocodile lacked in Alabasta. Plus Law's & Corazon's existence as well, they added an entirely different perspective to Doflamingo's character which Croc lacked.
I still prefer Doflamingo but Crocodile's not far off as well.