I wouldn't even say he put multiplayer or FPS in early because they're important, so much as it's just what makes sense.
When you're building something it's tedious until you can walk around and interact with it. I will not claim to be some kind of great programmer, but in my early 20s I did make a few different rendering engines (very rudimentary.) It's not fun work until you implement walking and interactions. Suddenly you can do something. When you code something new you can compile it and see it immediately. That's when coding an engine becomes thrilling.
So Notch created some boring gameplay, but it isn't the actual heart of the game, it's him running around so he has something to do in his new engine.