Clearing story mode earns you a decent amount of koins for buying unlockable fatalities, costumes, etc. in the Kombat Krypt. If you grow tired of this, you can use Arcade Mode to farm for koins.
Set the game difficulty to ''Very Easy'' and three rounds. Try getting a Flawless Victory (earns 1000 koins) each round. Perform a fatality for an extra 250 koins. This is a tedious but reliable method to earn a potential 3250 koins for a couple minutes of work.