I'd also go with the flight - the ease of the transit from international to domestic is a huge thing, especially compared to having to navigate trains in the morning.

I always urge people to think about their plans before buying a ticket - often times something like XXX-TYO-OSA (with a stopover in Tokyo) or XXX-TYO (ground transport) OSA-XXX is the same price (or marginally more expensive) than XXX-TYO (not to mention ground transport there and back!).