Having more chakra than someone else doesn't make you faster or stronger all of a sudden, it's how you use it to amplify your stats. Naruto has a lot of experience utilizing massive amounts of chakra to enhance his abilities, but Kaguya never really needed to learn to use her chakra to its full potential. Kaguya was always able to easily overpower her adversaries with little effort and therefore never learned to take full advantage of her superior energy reserves. Hagaromo and Hamura were able to defeat her with just a fraction of her power and some teamwork because they learned to utilize they power they had to its full potential while Kaguya threw her chakra around changing dimensions and making chakra fists but was ultimately defeated by the more sophisticated warriors. Upon being ressurected, she was just as handicapped by lack of real combat experience as the only real fight she fought was against her sons rampaging as the 10 tails. This is why Kaguya was an unimpressive shinobi despite having the most chakra.