Welcome, jd! Best thing to do with a new bike to find out what needs to be upgraded is to get on and ride the wheels off it. Weakness will become apparent. Address it as it becomes a problem. The important part is getting out a riding.
Like everyone else has already mentioned, ride, ride and ride some more. Until you have enough miles on the bike to figure out what works for you and what doesn't, I wouldn't touch a thing. The type of riding that you do and the terrain in which you ride will determine if upgrades (or a new bike) are in the future.
Welcome! The only thing that I would probably do first is to go clipless but that is only because I prefer it. Other than that, depending on what your plans are, you might want to make sure you are fitted properly to the bike and then ride ride ride. As others pointed out, the bits that you need to upgrade will become apparent.
As the others have said, get out an ride; maybe a proper bike fit will help you find a sweet spot. People say brakes, wheels, saddle, stem, pedals, tires, etc. Get a bike fit, get comfortable and get some miles in. You'll quickly learn where you and your bike are/are not compatible.