Some more conclusions-observations-advice:
1. If you are poor, but want anyway experience Japan - then it does not matter which is your starting point. Both Osaka and Tokyo and even Nagoya and Fukuoka provide you the experience of Japan, even if you could not afford JR Nationwide pass or stay in ryokans. For sleeping any business hotel is more than enough; just choose the hotel which maximum 15-30 minutes away from the major train station (Osaka-Umeda, Namba, Tennoji, Tokyo, Shibuya, Shinjuku). One week is enough to experience Japan and you can see why the europeans find Japan fascinating and why japanese adore Paris, Toscana, Iceland etc.
Just try to catch cheap airfare, use some regional pass (Tokyo Wide pass, JR Kansai Wide Pass) and walk as much as you can on foot i.e in big cities the distance between the 2 subway stops is not that long for a person who is physically fit.
Also, skip Disneyland and Universal Studios and focus on those sites which are aimed for locals and not owned by worldwide corporations. For example, Osaka Science museum, ferris wheels, temples-gardens, etc. These are all cheap i.e the price is less than 1000 yen.
2. When you are first time in Japan and first time in BIG train station - have some spare time! I strongly recommend for rookies to have at least 1 hour to spare when you arrive first time to either Tokyo, Shinjuku or Umeda-Osaka station. Those are huge and finding your platform might take time.
3. No problem at all if you do not have time to visit the must-see sights in Kyoto. Japan has plenty of temples and shrines, which are not crowded and the architecture is quite similar unlike the cathedrals-churches in Europe. Although in general - if you have seen one big cathedral, then others are also similar.
4. Food is cheaper in traditional supermarkets than in those huge food courts that are located in big departmentstores (Daimaru, Lucua, Kintetsu etc.)
5. Google Maps is an excellent tool to find temples, shrines, stores, beaches etc.
6. Bring or use cash. My Mastercard was disabled by my bank's automated security system, because it did not like, that JR West did 3 payments in row and also did not asked the pin during the payment process. Was not fun. Also, even the food courts in department stores might not accept credit-debit cards.
7. Again, 100% IMHO - but Japan does not have a Grand Canyon/Iguassu Falls/Cinque Terra/Paris etc type of sights. If you expect that you find such sights - you will be disappointed.
8. When do i have a 6th trip - never-say-never, but probably not next year (to have 4th trip in row). Daughter goes to school so that limits the time slots to have vacation and i have a temporary Japan poisoning :-).
9. And again - i am very thankful for the advice of other experienced posters.