My favorite Batman villain saw very limited use and it was called "The Wrath", they later brought in a similar character but I thought he was better. The storyline was called "The Player On The Other Side" (a Lewis Carol referance). The basic storyline was that on the same night that Batman's parents were being murdered by criminals, a family of criminals was being murdered by overzealous police. Where Batman inherited his family fortune, The Wrath wound up being dumped into reform school. Where Batman trailed with the best instructors money could buy, The Wrath trained with the elite of the criminal underworld. Batman swore vengeance on crime, The Wrath swore vengeance against the police/law and order.
The entire thing was a direct parallel in how they came to be, and how they trained, and the idea was that they were dead even in everything, the only way a fight could be resolved was when one of them eventually made a mistake. I thought the storyline was well written, though at the end The Wrath died, and was never to my knowlege brought back.
-
That said I like a number of villains like Harley Quinn, Poison Ivy, and even The Penguin because I feel kind of sorry for him.
Honestly though I think the best enemies are the ones who have had other motivations besides simple crime, or psychotic rage. I've long thought characters like Lady Shiva or Ra's Al Ghul were a lot more three dimensional.
As far as Robin's master plan goes, ironically another awesome villain that was only around for one storyline was "Azbat" as the fans called him. Basically after Bane broke Batman's back, he picked the hero Azrael to be a successor and put on the cape, but the guy went totally crazy. When Batman recovered he had to take his identity back.
I'm also surprised Cain was not mentioned. Cassandra Cain was my personal favorite Batgirl (apologies to Babs). Interestingly the fallout from Batman "adopting" her caused her "daddy" to come after Batman. He hatched a pretty awesome plan during the "Bruce Wayne: Murderer" storyline, and was a villain who had both brains and brawn. It also dealt with a gray area of "what ever happened to all these people who trained Bruce Wayne to become Batman". Cain was one of those guys, and Batman pretty much winds up letting him go for that reason despite everything. They have an interesting relationship.
Oh yes and then there was "Reverant Blackfire" (I think that was the name), a villain who literally took over all of Gotham long before "No Man's Land" in a storyline called "The Cult". He even brainwashed Batman after capturing him one night when he was a little too slow and got himself shot. Like "The Wrath" he was a limited use villain, and honestly I think he benefitted from that due to not being overused.
Well enough rambling, as I said, I think "The Wrath" was probably my favorite overall, but he is obscure, and very, very old.