I certainly don't think Hakone is a tourist trap. It's one of my favorite places in Jpn. And I definitely think Hakone could be done in a short time if you plan it well and limit where you go and what you see. I've outlined in detail the involved time frame in my post above. I've been going to Hakone for decades, and I've enjoyed it over half-day and over 2 nights.

Same could be said for Kyoto. If you want to see all major sights in Kyoto, it would take 3 days or even 7 days or more. However, if you just limit it to Higashiyama area and Gion and one other spot (eg, jaunt to Inari Fushimi), you could even do it on a day trip from Tokyo.