I think that we'll have to look at the motivations of the respective villains.
Joker changes his motivations on a daily basis. He's absolutely unpredictable and the chance of him killing me for any reason or none at all is just too high. I love the character, but working for him is suicide. A really exciting form of suicide, but the result is the same.
Scarecrow experiments with fear. And sooner or later, I'll get exposed to his fear gas. And I don't want that. There have been people exposed to his gas that never recovered. What use is your life without sanity?
Two-Face has a built-in 50% chance of abandoning the mission while it's happening and dooming all of his henchmen including me.
Penguin wants to rule the underworld, and I'll probably end up as cannon fodder in his gang war against Black Mask and Scarface. Thanks, I'll pass.
Ra's Al Ghul wants to wipe out the majority of the human race to create a better world. Even if I end up as one of his chosen ones to live in one oasis of serenity amidst a post-nuclear wasteland, chances are that most of the people close to me will not survive his victory.
Poison Ivy is even worse. She wants to kill every human on the planet and hand it back to plants. Nothing is worth that.
Which leaves us with the Riddler, whose sole motivation is to prove that he is more intelligent than everyone around him, including Batman. If I had to work for one of the Gotham villains, it would be him, while hoping that he IS more intelligent than Batman and this is all one huge long-term con, ending with us stealing a few hundred million dollars while Batman solved the latest riddle correct and ended up exactly where Eddie wants him to be. Like on a wild goose chase in Morocco or something.
Yeah. Riddler it is.