well actually you dont need to worry about that... its Japan, service is the top priority.. am sure the JR attendants will find a way to store your luggage..
JR PAss can you get you to all places where there is shinkansen, so don't limit yourself to just osaka kyoto and tokyo.. hehehe
anyways.. there are pros and cons, but JR pass is mostly pros , its convenient, its fast, get you to places in just hours .. go for it
my friend used it to visit from Kyushuu - Sendai and in between in 2 weeks.. how cool is that..