Overall, I enjoyed Arabasta more. I really enjoyed Baroque Works - their personalities make them my favorite villains in One Piece, period. I found the characters in Skypeia to be kind of bleh and I didn't find them to be very interesting. If the Skypeia priests got more screentime, I probably would have enjoyed them more. And the fights began to bore me after a while.
However, I liked the conclusion of Skypeia better than how Arabasta ended.