The very first thing Naruto did was save chocho and sarada using pure base foot speed against Shin who was fast enough to get away from Sasuke using foot speed. NO, Im not disappoint.
Naruto using the chakra mode was the best jutsu to use in that situation. Understand, Naruto's number 1 priority was the safety of the children. Naruto was facing a MS user with an unknown power that's strong enough to face Sasuke and escape from him using foot speed. Naruto didn't know what jutsu he was going to use. So by using the chakra mode it allows Naruto to counter any attack from any direction, while protecting the child, and staying focus on Shin.