You've got a couple different issues to look at when you consider getting a JR pass or not. You're frontloading your trip with Kyoto and Osaka, that changes the whole rail pass. I found that for the most part JR didn't go to the places I wanted to visit in Kyoto. I ended up using private rail/subway for the most part. Maybe connecting with JR to get a more direct hop to Kyoto station. On the other hand, in Toyko I was using JR almost exclusively. So, how much value will you get out of Shinkansen, NRT express and some misc travel?

The issue of baggage is really a matter of convenience vs money. If it's about money take the Hikari/Nozomi between Kyoto and Tokyo. Standard car is a 3x2 sear config. Green car is a 2x2 configuration. If you go during off peak hours it likely won't make a difference because it won't be that crowded. If you have a JR pass you'll be on the Hikari (no big deal).

On the other hand for convenience I'd use the Takuhaibin as much as possible and relax. Keep in mind you've usually got a 1 day lag. I recommend traveling with a small bag with a change of cloths and personal items. Toting around 1 or 2 small roller carry on sized bags is fairly easy.

Also keep in mind that people tend to pick of a lot of stuff in Kyoto/Osaka. Your bag won't get any lighter!