Why wasn't Jiraya able to use Sage mode completely? 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.
The title great Legendary Sannin does not mean theat he was the master of all types of techniques. He has sealing jutsus, summonings, body activation, combination techniques and is a pretty darn awesome Ninja. He did master the Sage techniques, he just couldn't perfect it.

Naruto surpasses Jiraiya as a Sage because of the nature of Sage chakra. It has to be in balance with the other two types of chakra in you. The balance was slightly tending towards Senjutsu chakra for Jiraiya and hence the toad like appearance, doesn't mean he didn't master how to use it.

Naruto mastered it too, but with the balance being perfect. Also, his clone training technique gave him 4 times more practice [exponentially more] than what Jiraiya was able to spare during his missions and travels. So it is possible that's a reason he was able to perfect it. Surpassing his master meant the perfect balance of chakra without any frog features according to sage Fukasaku.

They both were masters of Senjutsu, as they were able to use it without becoming a toad, were able to perform Kawazu kumite [excuse me if that's a typo] and giant rasengans.
HTH.