I do agree with you that the most problematic matchup for Conor would be a high level striker - particularly one with a very strong chin and a lot of cardio. If Conor fought a guy with a high level Muay Thai background (ideally one used to fighting with just wrapped hands and without gloves), who had been an MMA fighter for awhile and had good counter-grappling, that could be trouble for him - particularly one with good ranged body kicks which could drain him (I'm visualing a San Shou fighter, like Cung Le). A pure boxer would face a steeper climb - a fair bit of the head movement and defensive posturing, stances etc are countered by kicks/knees/elbows - but I personally would love to see more boxers transition to MMA while they still are young and healthy - and with guys like Conor making big money I suspect we may see some lesser-known and poor-drawing boxing champs come to MMA. Which would be awesome. Particularly if the UFC stranglehold ever cracks and they start paying the fighters what they deserve, we might see some of that.
As far as mixing phases of fighting, I agree that Fedor may be the best ever at it (argument for Jon Jones and GSP too, and a bunch of lower level fighters like Clay Guida and Kenny Florian etc were really good - Frank Shamrock and Bas Rutten long ago), but it's a continuum, not a "can do it/can't do it" kind of a thing. By the time a guy is rising to the top of his division he can usually do it really well - maybe not GSP level well but really really well compared to a regional pro fighter. Watching a lot of regional MMA this is what strikes me as the biggest difference. It takes a looooong time to get to that point and fighters young in their careers gas very quickly and are extremely awkward when doing this - it takes years and a lot of fights to do it well.
Although not the best at it, Conor actually is still a passable example of transitions making for more effective application, specifically because he doesn't have a wrestling background (although I would argue his MMA wrestling is still pretty darn good). Despite no background in it, in a MMA setting he is able to execute takedowns with good effect (unless he's completely gassed/rocked/dead, but very few can pull off a takedown under those conditions anyway) - he was really effective with his takedowns in the Holloway fight, and Holloway is far from being the easiest guy to take down with an 83 percent takedown defense stat at the moment. Conor's ground game is also under-rated, particularly his guard - as a BJJ player myself I was really surprised to see how well he did, sweeping a good Cesar Gracie blackbelt from open guard is no easy task (Nate still beat him that fight and is still the superior grappler, but it was a cool moment). Joe Rogan had an anecdote where Conor often will show up at random MMA gyms while training and join the BJJ classes and train with the best guys - most MMA guys don't do that.
