Never seen this "Warehouse" thing, but casting someone in bronze reminds me of the plot of The Mummy. You decide, for some brilliant reason, that death would be just
too lenient a punishment for someone. And so you bury them alive for all eternity. Utter genius. How could something like that possibly come back to bite you in the ass? It seems that it was done even worse here. At least Imhotep stayed dead for several thousand years.
I guess writing plots that don't hinge on people making idiotic mistakes is somewhat harder, since you need to actually make plans that work. And making a working plan for world domination isn't easy. And having the heroes counter a working world domination plan isn't easy either, since working plans are required to show some resilience to meddling by protagonists. A lot simpler to just have the bad guy use his turn-metals-into-soft-useless-gold-ray for robbing banks.
As for Batman killing the Joker... Maybe he's genre-savvy enough to know that he'd just come back anyway? Hasn't the Joker died several times already? Really, there's only so many times someone can fall from the roof of a building that then collapses on him before people around him begin noticing a pattern. At least they usually know about it when he escapes from Arkham Asylum.
Plus, shooting an enemy that just surrendered DOES kind of seem like a dick move, even if you know they are going to escape the minimum security prison you put them into. Maybe Batman should use some of his vast fortunes to improve the security a bit?