OK, adding on the list here are some ideas I've had.
Nightfall fragments on next orbital pass 10 years later?
Lucy is in 3rd world prison at very beginning
Lois is going to rescue her. This means that Superman starts off breaking someone out of prison, interfering in a governments actions.
Lois and Lucy are sent to live with an aunt in Smallville when parents divorce.
Lois has Bruce train Clark after Clark loses powers since he can't stop helping
Lois as something other than a reporter, something criminal like a cat burglar
Well's Victorian idea of utopia vs that of someone from the modern world?
Since Batman trusts Catwoman Clark reveals himself when needed even though Bruce hasn't yet.
Since magic works in L&C world maybe the Borneo Fertility statue is fix to the no children bit?
Clois survives, becomes a writer (novelist?), wins a Pulitzer before Lois does.
Doing something about New Kryptonians and lack of rights in that culture
Clark uses fake gadgets to make it look like he is human instead of using his powers openly
