normal rock kryptonite was also used in superman 3 - when Richard Pryor gives Superman as a present...
I'm not sure if it was used in Superman 4....
Kryptonite running inside Metallo or in Doomsday's blood is definitely more creative than usual, but it's still old.
It doesn't matter that kryptonite is one of Superman's weaknesses. Does every other superhero in the Marvel or DC universe always have a weakness? No, they don't - that's why you pit Super-strength superheros versus super-strength villains. It's not about a fight of winning versus losing. It's about the entertainment factor of watching huge fighting bouts - wrecking cities, smashing through buildings and streets, getting uppercutted into space, etc. a la final fight between Neo and Agent Smith in Matrix Revolutions. A person loses a fight due to being tricked, not usually being overpowered as in most hero/villain action movies.
Using Lois or the son as bait to pee off Superman is definitely good too - but any villain can do that - whether it be Luthor or Darkseid...If they are going to use kryptonite again, the villain should inject some liquid form of kryptonite into Lois or the son, so that Superman can't go near his loved ones, and just kick some villain ass already...