Why does everyone love Doomsday? Is that the only Superman villain you know of? Dude has no character or personality at all.
Mr. Mxy is way more intriguing. Metallo is pretty cool. Toyman can be downright terrifying.
Batman is a tough call. I've always just loved the Ventriloquist. Kind of a C or D lister, but dammit if I don't enjoy everything about him.
In terms of character, psyche, and well-written comics, I gotta give it to Scarecrow. If I have one complaint about him though, is that he's not very versatile. Here Bruce, have some more hallucinations about your dead parents.
Because not everything needs to be "deep" to be enjoyable. Doomsday is shallow, sure. But can you really not appreciate how one could love that simplicity? Doomsday exists to make bombastic awesome action and to look cool. Check and check. He is entertainment value, pure and simple. You can turn off your brain and just love to see him wreck shop.
And I want to echo your love of Ventriloquist: Nobody understands when I say how much I love that character. His psychosis is one of the most entertaining to me in the Batman mythos.
I guess light SPOILERS if you haven't read (I THINK) Knightfall,
But my favorite scene is when Ventriloquist gets Scarface back and Scarface gets into a fight with his replacement, Socko, and ventriloquist shoots up his own hands. That is just INSANE and I would love to see it on film