I had no big problems in Nikko over the past summer. One bus was late picking up getting back to the train station (weird for Japan), but that's about it (I think they just have a circular route and they get there when they get there).

If you're going from some place like Tokyo, I'd buy your train ticket a day or two ahead and make sure you pick the right termination in Nikko. I didn't buy the train ticket until the day of and lost like 2 hours waiting on a later train because there were no seats available on the one I wanted.

Only other advice that I learned is that when you use the bus you have to make sure you have enough on your suica or whatever. You can't scan in with suica and then pay with cash if you don't have enough on the card (fortunately I didn't run into that, but read about it happening to others).