If I am buying a new bike, the first thing I do is install clipless pedals and my favorite saddle, which is the Brooks B17. As for the rest, just ride and you will figure out what to upgrade next. Three years in, and I have switched out the following.

Upgraded the stock tires to Panaracer Ribmo.
Switched the brake pads to Kool Stop Salmon.
Replaced the stock back wheel to a 36 spoke custom wheel with a Velo Orange Grand Cru Touring hub.
Switched out the stock cassette from 12 - 25 to 12 - 27.
New chain, bought at the same time I installed the new cassette.