We learned in the Season 2 premiere that the two aliens had a falling out due to the fact that the D.E.O. has a cache of Kryptonite that Superman wants destroyed but J’onn wants to keep just in case a Kryptonian turns evil.
Assuming that Supergirl’s Metallo runs on Kryptonite in the same way as his comic counterpart, we might want to expect more tension between Superman and J’onn J’onzz.
The cybernetic body runs on Kryptonite; if J’onn had just allowed the Kryptonite to be destroyed, perhaps Metallo would never have been born.
Superman has happily agreed to continue hanging out with Kara in National City; that could definitely change if he and J’onn J’onzz have another big conflict.