The deal with Khabib is that many think he's over-rated and that he was fed 'nobodies' to fight which allowed him to amass like a 26-0 record. He has faced some good fighters, though,h like Edson Barboza, which he completely manhandled.
Some also say that Conor is over-rated, having fought a Chad Mendes, who accepted the fight on 2 weeks notice; that Conor got lucky in the Jose Aldo fight with the 13 second KO, and that he fought fighters who weren't in their prime(Max Holloway and Dustin Poirier).
As for the 2 year notice, it's interesting. Other fighters came off of a 2 year absence to win big, such as Dominick Cruz who beat TJ for the bantamweight belt.
Although it was 2 years since he last stepped foot in the octagon, it's been about a year since he last had a fight(Mcgregor vs Mayweather), the boxing match which allowed him to spend months training in preparation with his striking only(as opposed to learning a lot more stuff that MMA demands). Having gone through a boxing camp, I'd say his strikes may be a lot more powerful/better due to having a camp solely devoted to that aspect of fighting.