The biggest issue, is that Chronos rules the world now. And rules it WELL. They have done a lot for the world since taking over and a massive upheaval of the new status quo is not what they want to really do.
I mean, we just had Sho form a truce with the main Chronos faction at this point because they can be trusted for the most part. Of all the Zoalords, Shin seems to actually care about what the populace thinks of them, and doesn't just see them as rats to be stepped on, like Khan did. After the events of the Draglord fight, Chronos is on damage control.
So yeah, while a lot of people (in Japan especially) question Chronos, they are still the ruling body of the world... Even with diminishing Zoalord presence.
But sometimes, SOMETIMES, leaving a "bad" government in charge, is for the greater good of the populace.
I honestly bet, that after the rogues are dead, if Apollyon wasn't there, Shin could come to Sho and his group and essentially say " Hey, we'll essentially stop hunting you and allow you to live without hiding, just so long as you don't try to screw with us..." Sho probably would have accepted. Sure, they have done some horrible things to him in the past, but as of right now, the current Chronos is good for the world. About the only thing Sho cares about right now is his friends. If Chronos gave up on them, he'd probably not care about Chronos very much at all. Maybe even work with them to police the remaining leaders.
Of course then there is Agito and such... but even he is aware that strategy iis important in the case of trying to remove a leadership that new currently controls the entire world. Essentially what Agito seems to want, is to run Chronos himself. Agito's previous planning was all based on gaining more power to eventually take over. He had one final obstacle to his plan... And that was Sho. And Sho kicked his ass. If Sho had not won that fight, Agito would probably have tried to kill Shin by now, and still go after the remaining rogues.
This "Common Sense" you seem to believe should mean Sho and Agito should just destroy Chronos is essentially the issue the US has had in certain Middle Eastern countries. IE: they "Liberated" them from their "Evil" ruler and assumed they would be hailed as heroes. And that just didn't happen at all, and things are actually worse than before. How would you react to somebody who is essentially been labeled a Terrorist in ALL the media, suddenly swooped in and destroyed the infrastructure of the current ruling Government, who actually cured a lot of diseases as well as stabilized the economy of the entire world?