Of course, the tires and sealant need replacing, as do the drivetrain components of the cassette, chain and chain rings. I also replace all cables, housing, brake pads and bar tape. "That's just normal wear and tear, dude."
After careful consideration, the only upgrade is a new Velo-Orange Grand Cru crank set. When installing the new crank set, I find that the bottom bracket is a bit short. So, I replace the Shimano UN-55 square taper bottom bracket with another of the right length. I'll keep the still solid, shorter bottom bracket with the old crank set in the parts bin, just in case.
That's it, this time. Maybe I'll try a Salsa CowChipper handle bar in the future. And maybe a different saddle. Maybe. This bike is built for long miles on rough roads in all conditions. It handles that just fine.