Hi there,
The JR-Pass is indeed only available to visitors that enter Japan under a 90-day tourist visa.
The budget option for people that live in Japan is to use a night bus, prices for a standard seat start at around 3,800Yen between Tokyo and Osaka for a normal seat and are around 6,500Yen for a more luxurious reclining seat. Local travel between Kyoto and Osaka is not very expansive a one way ticket is 540 Yen by JR.
The Kintetsu Rail Pass is issued by the Kintetsu Railway which is a different company than JR, both have a different rail network. Also the Kintetsu Rail Pass is like the JR Pass only sold to people who visit Japan under a 90-day tourist visa.
It is possible to buy train ticket in Japan with a slight discount from discount shops
Also travel agencies in Japan may be able to give discounts if you book tickets on the Bullet trains and accommodations together. Lastly you can consider the Kodama economy plan that costs 9,800 yen for one way between Tokyo and Kyoto/Osaka, this is about a 25% discount over normal ticket prices and you get a free drink with it too, it does however need to be booked a couple of days in advance and sells out quickly in the weekend.
Hope this helps,
Daniel
