Why wasn't Jiraya able to use Sage mode completely?
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.