The JR Pass will be useful for travelling between major cities
connected by the JR network, but from what I can see, most of
downtown Tokyo and Kyoto are served by other non-JR railway lines
on which the pass is not valid. We'll probably end up getting day
passes for getting around on those local lines.
actually no need. just stick to the JR trains where your JR pass
will still be valid. don't waste money on the day metro passes
which are quite expensive unless you make many trips (7-8 trips on
average to make it worthwhile) in a single day.
especially within tokyo...the JR rail connections are pretty
good..one line - yamanote circle line - should get you to most of
the attractions...if not, within close proximities where you just
need to walk a little.
for some places not accessible by JR lines and you'd
really prefer to cut walking distances/time by taking the private
lines/tokyo metro, just buy single trip tickets. so the proposed
strategy (if you are traveling on budget) will be to use the JR as
the main mode of transport...and the non-JR lines for connections
if need be.
for kyoto, as i've mentioned, you are better off taking buses.
i've travelled extensively with JR passes without the need to pay
to travel on other subway lines i.e. tokyo metro, other private
lines.
http://www.jreast.co.jp/e/info/map_a4ol.pdf -
refer to this for all the JR lines within tokyo/greater tokyo. you
should find that you can get around the whole of tokyo with just
these lines...and using your JR pass.
http://www.jreast.co.jp/e/routemaps/pdf/RouteMap_majorrailsub.pdf -
refer to this for all JR and non-JR lines. JR lines are in
black/white.