Unless you ride in the rain often, I wouldn't bother with disc brakes, and as others have noted, especially as an upgrade, it is not cost effective because of the number of additional changes needed.

I would suggest a tire upgrade to the best tire for whatever conditions you ride. I ride a lot of crushed stone and gravel, and some pavement, and I notice that my current favorite tire is available on Amazon, the Clement X'Plor USH. It is 35mm, and I am riding the 60 tpi version, but my next tire change on that bike will be to try the 120 tpi version, since they should be even better. They roll well on pavement, but provide a great ride and traction on crushed stone and gravel. I ride almost exclusively in dry conditions, so I can't say how they perform in the wet... But, even if not these tires, there is probably a high quality tire available that would fit your needs and be a definite improvement.

Along with the tires, there are two components that are relatively crappy on almost any new bike because many riders have their own favorites, and they are very personal choices... Therefore, you may want to consider a better saddle (unless the one you have works great for you), a nicer set of pedals, and possibly (depending on your spending limit) get shoes and go clipless.

Almost anything else, unless required for your riding style (lights, rack etc) is probably not gong to be cost effective.

Whatever you decide to upgrade, enjoy the ride!