If I'm playing one of them online in 2020 I'm going to MK11 and not even questioning it.
But I think MK9 is the best overall package for its time. As a competitive fighter, it's not the best, but it still had a very hype tourney scene. But more importantly, it was just a great game. The music, story mode, single player modes, characters and overall cohesion were the best. IGAU didn't really look or sound good. MKX story mode wasn't great and the initial roster didn't really pop off. Injustice 2 didn't have great single player modes and the gear felt tacky. MK11 story mode was up and down. MK9 was a more cohesive and fresh game for its time and that's what the greats are remembered for IMO.