They are completely different characters, one is a younger Kal-El, one is a clone. Both share a few similarity, they carry the S and they're telling story about a younger "S" symbol carrier with path to pursue upon, to learn.
A lot of struggle the characters faced were template for a beginning stage history.
Their powers are both constrained, and that's part of their character. Only with the young Kal-El, he's on the path of growing to have Superman's ability.
With Young Justice's Connor Kent, he has a darker history with a slight twist that Superman doesn't have, his appearance will never age.
Similar ability stats: Both can't fly, both are allergic to kryptonite.
To you, who has the more interesting history as a young S carrier?