Here's divisions on the map which are not isolated on turn 1 in a game against the AI:

There are 23 divisions with morale <40. There are another 6 with morale >40 but experience <40. There are still another that are not much better with both morale and experience between 40 and 45. And what is more, you get even MORE low morale (and barely equipped) tank divisions popping up in places like Rzhev in a few turns.
So a big part of the first turns (especially turn 1) for the Soviets is figuring out what to do with all these low morale, low experience mobile units.
On the one hand, you don't really want these in combat while their morale and experience is so low. They will fight very poorly, and you will lose AFVs that could be more useful around turn 10-15 or so. What is worse, if they get isolated and surrender, Germany can capture a lot of vehicles. On the other hand, Soviets need all the counters they can get on the map in the early turns to slow down the Axis advance, and you can try to put them in (relatively) safe positions so that fewer of them will actually end up in combat, while providing some extra depth to your defense.
So what is the least bad out of the various bad options?
1) Disband:
You can disband at least a few of the very worst of them.
pluses - Gets more equipment into better units, which can get higher TOE with more AFVs.
negatives - More undefended hexes that Germany can just walk into without even having to deal with a ZOC or combat delay.
2) Send them to the front (but put them in locations where they are less likely to get into combat):
pluses - You need depth in your defense, and these can add a bit of that. Some may end up in combat and doing badly, but probably most won't, if you are careful enough. But the extra counter ZOCs could help stop a German breakthrough or encirclement.
negatives - They will recover morale and experience very slowly on the map, and at least some of them will probably end up getting beaten up (and give Germany some captured vehicles) even if you are careful. They also generally have low construction values, so while they will build some fortification, it is not that much.
3) Suicide them:
pluses - You can probably cut off some German Panzers and slow down their advance a bit. Also, if you suicide them early, they will have fewer vehicles for Germany to potentially capture than if you suicide them later.
negatives - Germany can capture potentially a large amount of vehicles, and the AFVs will hypothetically do less damage to German Panzers than if you wait and use them to attack Panzers later.
4) Send to National Reserve:
pluses - Morale (and experience?) should go up more quickly than if they stay on the map. No risk of losing AFVs or captured trucks before they are combat ready.
negatives - With fewer Soviet counters on the map, it is all the easier for German Panzers to run rampant. They also won't gain CPP or dig forts. You also don't get credit towards TB requirements for having them in theatre boxes.
5) Send to the Transcaucasus:
If playing with enhanced theater boxes, you can send some tanks to the TBs.
pluses - No risk of losing AFVs or captured trucks. You get credit towards fulfilling the TB requirements while morale/experience is going up, and later (if you want) pull them back to the map when they are more combat ready, and potentially when Germany is more vulnerable.
negatives - It takes two turns for them to arrive, and then another 2 turns for any replacement units to come back. The first few turns while you are waiting for TB transfers to occur are also the turns when you most need more counters on the map. Units regain morale/experience more slowly (I think?) than in the national reserve.
6) Send to the Northern front:
Same as the Transcaucasus, but you will lose some equipment in simulated combat.
pluses - You can't send everything to the Transcaucasus, and this has more capacity.
negatives - You will take some combat losses when Finland attacks. You also may want to have as few units as possible in the Northern Front TB until Finland gets the event to stop at the Svir river so that the period of high combat intensity can be as short as possible.
7) Send to the Northern front:
Same as the Transcaucasus again, except it takes 2 extra turns for units to get there and back (each way).
pluses - You can't send everything to the Transcaucasus, and this has more capacity.
negatives - It will take quite a long time to get any units back to replace what you send there. With 4 turns of transit time, during those 4 turn periods you also won't be benefiting from credit toward the TB requirements.