There are plenty of things that can be done to improve Pedal-Pi, most of them are software. The major limitation right now is using the Raspbian OS which is great because for its simplicity but the OS load (memory management, interruptions, etc) can affect the sound quality.
Be aware that all the ideas mentioned below require good skills of linux/embedded programming.
Baremetal Programming: Complex but gives total control of the board resources:
For any of the alternatives mentioned above I encorage to do a google research before starting, there are new ideas and improvements in these fields every month.