love create-react-app, to get up and running but I've never liked keeping it that way.. I've found ejecting and forging forward from the base react app is best.
having access to the webpack config to set things up the way I like and such. I've also had issues with getting SCSS to work before I eject as well pretty continuously through the versions.. not sure why.
What things in create-react-app are not the way you like? Maybe we can make them better for everyone. :)