The Super-8 teams should have played each other twice. Look at India, lost 1 game, and out of the semis. The run rate should not be the default picker for the semis teams. It should be wins. But that's not possible with so few games.
Have two groups and pick top 3 from each.... 6 teams - play with each other (leading to 5 games each) (see if carry over points from leagues should be good idea or not), post five matches, pick the top 4 for semis and then knockouts to final. Play 3 games for final.