How could Jiraya use sage mode by holding his hands? So Naruto can enter sage mode in a matter of seconds but he has to be completely still. But Jiraya could use sage mode with only using his hands but it took him a long long time to achieve it..why the difference?
You are not right with that Naruto can enter in sage mode in just matter of seconds, It also take time to gain sage chakra from nature for Naruto.

There are some condition to gain sage chakra from nature.


  In order to gather enough natural energy to initiate the
  transformation into Sage Mode, the user must remain perfectly still.


To overcome this weekness, Jiraya use
Sage Art: Amphibian Technique, where one or more toads fuses with the user's shoulders and gather natural energy for them to use. 

Where Naruto Use his shadow clone to gather nature energy and call back his clone to his original self to gain sage chakra. but there is limit of shadow clone he use is 5.

You can find more details here.