While I understand that supersoldiering and the inevitbale pitfalls involved have become a storyline cliche, I submit that The Joker is the one (and probably the only one) villain for which such a supersoldier project does make sense to implement.
The difference between The Jokers and most if not all other SS plots is that the usual creator of such a scheme is someone whose only known scheme is the SS project in question. Basically, the usual villain du jours entire body of work as we know it involves only this project; the one project important enough to make a game/movie/book/etc about.
The Joker has thousands of various schemes under his belt! He's done about everything that a supervillain such as he can do, and, honestly, if you offered the Joker the means to create such an army of SS, do you think he wouldn't take it? Hell, he might have found the whole thing innovative, and even if it didn't work, he still gets to test Batman for the umpteenth time.
Bottomline: Take away the Joker, supersoldier is a cop out, but I could buy the Joker's involvement with this one, especially considering some of the other details of his scheme (buy it, play it, love it).