Looking at a political map of Russia
http://www.russiamap.org/images/full/political-purp.gif
most of the urbanisation is in European Russia, Asian Russia has vast tracts of open territory. I can't think of a tactical reason why the USSR would station valuable troops (at least, not in any significant concentration) in the middle of these open spaces, when the threat would almost certainly come from the west.
This has two aspects that favour the Axis, it will be just as hard to meet the invasionary force as it would be for the invaders themselves to make progress - just as the Japanese have to advance westwards, the Soviets, if they intend not to disregard the threat from the east, will have to transport troops and equipment to a point where they can take the war to them.
Secondly, with the US not about to descend upon them, the Nazis would likely take European Russia, assuming Hitler doesn't do anything silly like committing resources to urban warfare etc. With the most densely populated area fallen (along with the capital), Asian Russia would fall piecemeal. The WWII Soviet Union was bereft of the same standards of communication into mid- and far eastern Russia, which was populated almost entirely by peasants.
The bulk of Soviet forces would be highly likely trying to protect the European (capital city-containing) Russia, the Japanese could contend themselves with being the largest nuisance raider in history, knowing that Soviet interference would be just as difficult for the Russians as invasion was for the Japanese. There would likely be provision for rudimentary airstrips in Asian Russia, these would be difficult to find for the Soviets, whilst the Japanese aircrews knew exactly where the Soviet airstrips were.
If the Soviets committed enough resources to settle the Japanese problem, they'd leave themselves wide open in European Russia, if they didn't, they might even have trouble locating the Japanese in the quasi-10th century wilderness of the interior and far east.