What are the things that you will usually replace in a ARF kit ?

For me, I would strengthen the joints of Epoxy and CA. Note: CA are expensive and probably factory will try to skimp on that.
I would also replaces the Clevises and pushrods (if they are bent).
Replace the fuel tank with Du-Bro. Check for air leak.
Seal any exposed balsa with clear covering.
Make the planes lighter and drilling holes through low-stress frames.
Sometimes, replace the motor mount with Dave Brown mounts and even re-construct the firewall if necessary.