why are they doing it? cause its the DC universe and other characters beside clark are cool, and makes for him being apart of something later seem bigger and better. it also just makes for interesting episodes. but mostly people want to see other characters besides clark.
second, clark DOES NOT get his powers from the meteor shower, he is a Kryptonian from Krypton. he gets his power from being a Kryptonian.
see kryptonians have super powers when they are near to a yellow sun (like earth has) they're cells absorb the yellow sunlight and it gives them super abilities.
Clarks super powers are not the result of the meteor shower like everyone else's.
They dont really explain how Jor-El can take clarks powers away, but it could be the result of many things. maybe he alters clarks cell biology so that they do not absorb sunlight anymore. who knows