First of all - I'm going to be giving away a very minor Arkham Asylum spoiler in this article, so if you're one of the three very stupid people who haven't bought it yet, close your eyes and stick your fingers in your ears until the end of the page.
If there's one videogame plot device that gets aired an awful lot, it's supersoldiers. By that I mean, plots which involve the villains creating or turning existing soldiers into massive super-strong killing machines with shoulder muscles the size of armchairs, so that they can be used as an unstoppable fighting force. And as I may have already made clear on several occasions, I do wish that game writers would pack this shit in.
I can understand that it fits well into the gameplay/story balance. It means having a decently upgraded enemy for when the difficulty curve rises. It provides a platform from which boss monsters can be easily created (generally by having one supersoldier take twice as many vitamins as everyone else). There's absolutely no guilt to be had in killing supersoldiers, nor the God-playing megalomaniacal generals that created them. And with supersoldiers come all the nice, safe, usual trappings - laboratories, mysterious machinery, big glass cylinders with dudes floating inside them and everything else that keeps the whole scientific folly theme ticking over.
But here's the thing - creating supersoldiers doesn't make the slightest bit of rational sense. First of all, you're basically creating an entity whose only purpose is to fight, so what the hell are you going to do with them during peace time, pack them in a box? And this is assuming you could even control them. If they haven't regressed to a slavering bestial state or been driven insane by the monstrosity they have become, how are you going to make them do your bidding, Mr. Small Fragile Human General? You really want to start issuing threats that might come back to haunt you when some leashes get slipped? To say nothing of the fact that the ethical lapse involved would be ruinous in a country where people fight for the rights of embryonic cell clusters, and that most supersoldiers could be effectively countered by, say, dropping a great big bomb.
It's at the point that whenever a game villain brings up a supersoldier project, I immediately realize that they are an absolute cretin, thus destroying all perceived threat. It makes an especially small amount of sense for the Joker to pursue such a scheme (whoops, there goes that spoiler I mentioned). The leading cause of Joker henchmen death is the Joker's own boredom threshold. I really don't think all his henchmen being the size of forklifts would ultimately work in his favor.