8days travel from Osaka to Tokyo

I've just settled booking all my hotels.
a) Dontobori Hotel in Osaka fr 16/2/13 reach KIX airport abt 10.40pm then check out on 18/2/13
b)Best western hotel in Kyoto from 18/2/13 to 20/2/13
c)Shinjuku Washington hotel in Tokyo from 20/2/13 to 23/2/13
d)23/2/13 will leave Tokyo fr Haneda Airport at 11.45pm
From the above hotel booked,
1) what is the best route to take from one place to another & whether to buy any sightseeing pass?
2) According to my limited time, any good suggestion where to visit in Osaka, Kyoto & Tokyo base on my hotel location.
3)Shall I goto Hakone when I'm on the way to Tokyo (with my big luggage bag)or do it when Im in Tokyo?which way is save time & money?

1) what is the best route to take from one place to another & whether to buy any sightseeing pass?

Kyoto access (choose to/from Osaka and to/from Tokyo)
http://www.japan-guide.com/e/e2363.html

Depending on what you see maybe a One Day Bus Pass in Kyoto (500 yen) will be useful. For the rest I'd just pay for individual tickets.

2) According to my limited time, any good suggestion where to visit in Osaka, Kyoto & Tokyo base on my hotel location.

What are your interests? Please read each of the city guides, look at some of the suggested day itineraries, and pick places of interest:-
http://www.japan-guide.com/e/e2157.html
http://www.japan-guide.com/e/e2158.html
http://www.japan-guide.com/e/e2164.html

Feel free to post back if you want advice on how to co-ordinate places of interest.

3)Shall I goto Hakone when I'm on the way to Tokyo (with my big luggage bag)or do it when Im in Tokyo?

Up to you. You can also consider shipping your luggage from Kyoto to Tokyo:-
http://www.japan-guide.com/e/e2278.html

You could also go from Kyoto to Odawara and store your luggage at Odawara Station in the coin lockers there and just collect it when you continue on to Tokyo.

Because you don't seem to stay overnight at Hakone you may prefer to keep Tokyo schedule flexible and head to Hakone if the weather is good to improve your chance of seeing Mt Fuji.

which way is save time & money?

Obviously you save time and money if you stop at Hakone on the way to Tokyo.

Enjoy your trip!

Thks GC3, let me go through & get back to you....I think Im still very confuse with the transportation..