1944 army without combat experience, without any of the developments in tactics they gained fighting the Germans, and without the bad generals being weeded out and good ones promoted as completely as they were by war. Also, no Lend-Lease aid for their logistics.
A major component of Timoshenko's reforms was the graduation of a new, professional, and experienced officer corps which would have filled out the Red Army's ranks and replaced those lost during the Purges. Many shakeups were due in the high command during this period. Further, much of the Red Army's tactics in 1943 and 1944 were actually Timoshenko's reforms adopted ad hoc into the Red Army between 1941 and 1943. There were some changes to contend with new strategic realities, but most of the basic changes he got approved were those that vastly improved the Red Army tactically later in the war.
I can too, primarily due to flaws in how their formations are structured, namely that they were too rigid and inflexible for a proper mechanized assault. I can also see them underestimating how fanatical the Nazis would actually be in the scenario the Nazis would be facing and running into several buzz saws from that. But this is more the Battle of Rhzev than Third (or especially Second) Kharkov, and the Germans will never win a war with Rhzevs. Especially not in this scenario, instead this gives them an overland Pacific war: start with a bang, end with a whimper.
I can't see a Rzhev coming about. Rzhev was prompted by a variety of factors, including only partial implementation of the Timoshenko reforms, a lack of a real officer corps, and generally poor quality men and equipment. This was further caused by the massive losses of Barbarossa, which set back Timoshenko's reforms by several years. Without that the Red Army will be better disciplined and able to operate more smoothly, especially in cooperation between artillery, infantry, and armor.
The Soviet army will have to deal with the same partisan and logistical issues that Germany had. Their morale and determination will also be nowhere near the same as IOTL because they aren't fighting the Germans who've raped and butchered half their country.
Partisans? Definitely not. The Soviets were far more effective at rounding up possible resistance groups and organizations than the Nazis. Plus they'll be occupying lands which are 1. Geographically constrained and 2. Less populated than the Soviet Union and 3. Population is much more concentrated in urban centers. This leads to the easy suppression of dissidents. Logistics will certainly be a problem but unlike the Germans the Soviets will be able to easily secure they rear areas which will facilitate rapid conversion of rail lines. Their logistic planning will also be much better; the Winter War taught them the merits of proper supply organization. I disagree that motivation will be that much less than IOTL; from day 1 of Barbarossa the Soviets resisted ferociously and showed no mercy to any German prisoners taken. This is well before shit really went down. The Red Army was quickly becoming a disciplined force, both fear, training, and simple indoctrination.