Hello!

My wife and I are going on a trip to Japan. The plan is:

Tokyo>Hakone>Kyoto>Tokyo with some day trips in the middle.

My questions is how to use the rail system and what makes the most sense. Should we just get the JR pass? Or is there another option that makes more sense like the Romancecar? Anything would be helpful. There’s so many different recommendations out there.

The JR pass is no longer worth it for your itinerary. The Romancecar is only a good way to get from Shinjuku to Hakone or Enoshima. The Japan guide is a good source for information about visiting Japan

When you leave Hakone for Kyoto be sure to take a Hikari shinkansen train bound for Kyoto or Shin Osaka.

It used to be that the cost of a one week JR pass was about the cost of a round trip ticket between Tokyo and Kyoto so worth it for an itinerary like yours as you could also use it in Tokyo for local trains. Unfortunately the cost of a one week pass just increased in cost about 70% this month so no longer worth it for most people. Also the JR pass does not cover the Romancecar.

From the discussion it seems like the JR Pass may no longer be the best value given the recent price increase. I'd recommend just buying point-to-point tickets as you go. Definitely get a Hakone Free Pass though to cover buses/trains there. For Tokyo-Hakone, the Romancecar is a nice way to go. And for Hakone-Kyoto take the shinkansen. You can look up schedules on Jorudan. Have a great trip! Japan's rail system is super easy to navigate.

I wrote a webpage on these topics. See if you find it useful:
https://adumbrate.org/pics/traveltips.html#trains

Excerpts: There are many kinds of train passes in Japan. There's a description here: https://www.japan-guide.com/e/e2357.html

https://www.klook.com sells discounted train tickets. I've not used them myself and don't know how reliable they are, so you'll need to do your own research on that.

The low-cost airlines in Japan (e.g., Peach, a subsidiary of ANA) can be very cheap (much cheaper than train for, say, Tokyo-Osaka), and frequent flyer tickets on JAL and ANA are usually readily available and are a very good deal (typically only 5,000 miles or points from One World or Star Alliance, respectively). ITM is the in-town Osaka airport (cf. Haneda for Tokyo) and KIX the distant one (cf. Narita).

I'd suggest flying one way between Tokyo and Osaka/Kyoto or vice-versa to connect up with your international flight (possibly overnight at an airport hotel). Or just book an open jaw ticket.

klook is good. I booked a couple of regional rail passes and a sim card through them. Cancelled the JRK pass and got a prompt refund. I forget why I cancelled the Kyushu pass. Was able to use the klook-booked JR East pass to reserve a seat on the JRE website.