A lovely trip. First day you see Fuji, Hakone, Boat and cable car ride. Scenic's are gorgeous (on a sunny day). Bullet train that night (for 1 nighters), or stay overnight. Next day, you're on your own, hard if you don't know Japanese. But the sights are wonderful. I say worth the 2 days.
It is what it is. It's a city tour. You get to see a few sights in the 3hrs you have. The tour guide was really good... very informative and answered questions we had regarding culture, history, education, economy and politics. If you want a quick tour during a layover type stay, then try it.