There's actually two problems:

1. The reservations for any subsequent segments on the same ticket will get automatically cancelled when you no-show for a segment, including any return portion.

2. Separately, the unused value of the ticket can't be used for rebooked flights unless the coupons (aka each segment of the ticket) are used in order, or you rebook the whole thing to a new fare that has just the segments you want to fly and reprice the whole thing.

Try pricing out the flights that you want to take: arriving in Tokyo, and departing from Osaka and connecting through Tokyo back to your point of origin. I think you'll find the price of that is dramatically higher than what you've found for your roundtrip to Osaka. That's the price the airline expects you to pay if that's what you fly. If it was easy to implement what you suggest, everyone would do it that way and nobody would pay the full price.