Most standalone Marvel films are an origin story in some way.

Black Panther wasn't T'Challa's origin story - it was Killmonger's origin.

But wouldn't he have basically come to that conclusion already considering what he endured in Civil War?

In Civil War, T'Challa learns the difference between vengeance and justice.

In Black Panther, he learns the difference between justice and mercy.

This:

But here we are in his stand alone film where he's more or less learning that same lesson all over again albeit with less of a ticking clock involved.

is the key - Black Panther isn't about T'Challa's journey. It's about how Killmonger rejects the lessons you've identified.

Killmonger's rise and fall shows T'Challa how bad Wakanda is/has become and convinces him that it needs to be reformed.