On all three of my Japan trips I used the ordinary JR Rail Pass and never once felt the need or urge to upgrade to green. (once considered getting a JR Kyushu pass but it didn't make sense for my plans) I'm 6ft and not slim and was perfectly comfortable. In terms of luggage, I advise people to pack light and use small-to-medium roll-aboard suitcases, and if you can't stick to that due to habit or circumstance, take advantage of the excellent luggage delivery services country-wide. The shinkansen system is better-than-world-class and they are still opening new lines (completed the Kyushu line a few years ago and are opening a new line this Spring) and upgrading the trains themselves with newer models! From my experience and what I've read here and elsewhere, the views from the trains are better than the views from the expressways - in general. Spend a few days on the rail system and you get why rail fans are legion in Japan. In terms of flexibility, most of the bullet train lines have trains going at least every half hour to hour, so timing is less of an issue than location coverage.

I agree with the general consensus to stick with rail and public transportation, and rent cars in specific places where it makes more sense to do so.

I do like the idea of a road trip for the service area experience, but that would be a very specific kind of trip, and most likely not for the first or second-timer. Just a hunch from the questions that the OP is a first-timer...