The main challenge with the KID is that most White's options are challenging in some way. I think the following game was a big blow to the system's popularity:



So the top players often go for ...Nbd7/...Na6 setups, but objectively he is conceding a small positional edge to White in these lines. Nothing to stop you playing this at lower levels if you like the positions, but against a top GM with preparation, you will suffer. 

It's a strategically risky defence where Black is playing to win. So more appropriate for an open Swiss than a top level all play all maybe .

Nakamura seems the KID torch bearer at the top at the moment. I loved his win agaist Wesley So. But even he is using more solid defences like the QGD and QID.

Has Magnus Carlsen used the KID at the top flight?

Until Gata Kamsky unexpectedly played the King's Indian today in the US Championship, we haven't seen it much in recent high level tournaments.  No KIDs in the Norway tournament so far  or the Candidates.  It has only appeared once so far in the Chinese Championship.  We have to go to the Schachbundesliga in order to find many KID games.  Perhaps Shipov was right when he said at year-end 2015 that the King's Indian is getting harder to play at the highest levels.  With deep computer preparation plus an understandable emphasis on solidity with the high stakes of some of these tournaments, there aren't many top players risking it.   

Which variations do you think King's Indian players are most concerned about these days?  The Makoganov with 5.Nf3 and 6.h3 has been doing well.  There have also been some strong games for White with the Bayonet and even the Petrosian variation.  The Fianchetto variation also continues to be solid for White.