As shown in Shippuden, Fukasaku, one of the two Great Sage Toads says that Naruto has surpassed his master.
Jiraiya was not able to completely enter into sage mode, and as such only had a partial toad-like appearance.
This is what I read from Naruto Wiki:
Jiraiya didn't like Sage Mode because it gave him a more toad-like appearance, with longer marks along the sides of his face, a goatee, a larger nose with warts, webbed hands and feet and sharp teeth, all of which made him unappealing to girls. This appearance is due to Jiraiya not having complete mastery over the technique.
But I don't think this was the only reason for not mastering such a great technique.
Even though he was one of the great legendary Sannin, why was he unable to master the Sage mode completely? Any reason other than the above.