Tough one. I actually like the sequences in Casino Royale better but I don't think they're very cohesive - the casino stuff feels like a completely different film to the plane plot with only a thin link. Then you're left wondering why the film isn't over yet before a whole new eyepatched villain shows up for a tacked on climax.
Skyfall while I don't think it hits the same heights is better as a whole so I'd go for that.
Casino Royale is in my top 3 and definitely a better movie. It's one of the few Bond movies I give 10/10. Skyfall was great too and in my top 10 but it has the one gaping flaw with Silva's plan and Q being stupid enough to plug Silva's computer into their computer. I would give Skyfall a 9/10.
Skyfall ; it's also my #1 Bond movie straight up and within my Top 20 movies in general.
-It's paced better overall and holds my all around interest more. Casino Royale is not at it's best til around Eva Green shows up which is about 55 minutes into the movie.
-It's visually superior as Sam Mendes/Roger Deakins combo will be difficult to beat when given the right kind of subject matter like this. NOTE: although 'Road to Perdition (2002)', which is also directed by Sam Mendes, is my 'go to' movie when I think top notch cinematography/movie combo (Road to Perdition is within my Top 8 movies straight up).
p.s. Skyfall is my #1 Bond movie and Casino Royale is my #2 Bond movie of them all. NOTE: I re-watched both on Nov 8th and 9th of 2018.