The notion that the Soviet Union would be devoid of units at any time in the war is just silly. Between June-December 1941, the Soviets mobilized almost 10 million reservists and volunteers. They lost about 6 million in the same time period so they almost doubled the size of their at start forces in 5 months.
To clarify, and I'm also not disagreeing with the above, mine was just a commentary on the current in game situation explaining what might be happening for the AI.
However, in game terms, any lack of "on map" defenders after the initial Axis assault is really only temporary, and more of a functional abstraction representing the core loss of effective combat units in the short term. Their delayed re-appearance, as well as newer units, back into the game reflects the time needed for reorganization, restrengthening, and replacement of units back into the field. This abstracted disarray on the Soviet side (after the initial wave of the Axis assaults) also allows for the Axis to maintain their timelines, i.e. their blitzkrieg forward into Soviet territory as otherwise it would be very difficult to reach historical objectives by the end of 1941 at the current game turn lengths.
Essentially the Soviet manpower is still there, it is just in this game represented by not only units on the map, but also units being rebuilt and built and reflected in the delayed time it would take to get them back into the field. For example, many destroyed units can be bought back at reduced cost and at a reduced production time to reflect this.
That being said, there are ways to do it differently, however it would require probably 4 times as many turns in a year (if not more) as well as combat values adjustments and then there would be no way to have the overall game length play out in quite as an enjoyable and reasonable time frame. You would have increased unit concentrations, not necessarily a bad thing as this does eventually occur by war's end, but I doubt you'd have as much of the "tactical" feel that the game offers, and at this strategic level which many players seem to enjoy quite a bit as well. For example, that blitzkrieg re-creation feeling you get in game at the start of Barbarossa as you sweep through the USSR and so on.
Sometimes it is a careful balance, to get playability vs history just right, but I think you'll find that it plays out quite well overall.