I have been browsing Pinoyexchange and with the easing up of Japan visa application, coupled with the additional flights that go to Japan daily, a lot of people are thinking of going to Japan. But before hitting the BOOK button of your favorite airline, you gotta make up your mind. If Tokyo has Disneyland, Osaka has Universal Studios. Tokyo has Imperial Palace but Osaka has so much castles and palace on top of the Osaka Castle sitting in the middle of Osaka Business district. Tokyo has Mt. Fuji (or at least near Tokyo) and admittedly, Osaka has nothing to match with the beauty of Mt fuji.
If you intend to visit both Osaka and Tokyo, you will need a minimum of 7 days. And a whole lot of money. There are pros and cons of doing this but if you will ask me, both cities have different appeal. In Tokyo, the biggest plus in going there is to see Mt Fuji which is just an hour away by train or bus from Tokyo (note: see my earlier entry on going to Mt Fuji by bus). However, if Tokyo has Mt Fuji, Osaka or Kansai region has Kyoto and Himeji: two awesome places that is so difficult to have a counterpart in Tokyo.
Note that Tokyo is far from Osaka but if you have the time and money, you can take a Willer overnight bus from Osaka to Tokyo. Your other choices include plane (this is expensive and you gotta consider the distance of the airport from the city) and the shinkansen.
Plane travel from Osaka to Tokyo, especially if you will land in Narita, is really not an option because for one, Osaka-Kansai airport is far from Osaka (unless you are leaving from Osaka-Itami Airport since this is nearer Osaka). Even worse, if you land at Narita, it is very far from Tokyo and you will end up taking more than an hour on the train just to get to Tokyo.
This leaves you to the last option: the shinkansen. The shinkansen departs from Shin-Osaka Station (DIFFERENT from Namba station as this is the final stop of the Nankai Limited Airport Express and Rapit and Osakanamba for the JR line). Last I checked, a one-way ticket from Osaka to Tokyo is JPY 14,500 for a 153-minute ride and a distance of roughly 600 kilometers.
So here's a very important piece of advice: if you intend to do both Tokyo and Kyoto, make sure to get a split ticket: Manila-Tokyo-Osaka-Manila or Manila-Osaka-Tokyo-Manila so you need not return to your port of entry just to get home. Also, make sure you buy the JR 7-day pass. The shinkansen fares alone between Japanese cities are so expensive that you are almost sure to get more out of your pass than to individually buy your ticket without the pass.
Now, if you will ask my opinion, I would say one city at a time. You will be overwhelmed with what you will be seeing to the point that you will not appreciate the place. Take a 4-day trip to Osaka and then schedule a separate 3 or 4-day trip to Tokyo so that you will not bombard your senses too much.