I don't think Nate is the better boxer at all. And no timing doesn't beat speed everytime. It's not that simple.
And those cuts were legit game ending cuts. Conor knew that, and probably got even more cocky. He knew he had the fight in his pocket.
Nate was always circling away so those big shots from Conor weren't having their full effect. But, if they were fighting with boxing gloves, in a traditional boxing match, I think Conor would win pretty clearly.
I think the problem is just Nate was too big for Conor. Nate is more of a WW than Conor is. That size difference can make a huge difference. It's what allowed Conor to get hurt so much more easily. It always seemed like a slightly bad idea. It also means to damage the guy you have to hit him many more times than usual, opening you up to extra risk.