Generally speaking I don't think it is worth it.

The luggage space is the same (I guess you can say it has more because fewer people are sitting in the car, but I never had a problem with ordinary carry-on luggage in the ordinary car), and the ordinary car seats are just as comfortable. The green cars are just a little more posh, 2-2 seating vs 2-3 seating on the Shinkansen (seating configuration maybe different on other trains), no real difference in leg room, just a more padded and wider seat and a footrest. Not all trains have green cars, especially if you plan on doing a lot of travel on the Sanyo Shinkansen, also as mentioned not all green cars are created equal, depending on train it can just be the same as regular cars you'd find on other trains, or it can be nicer.