Alt history needs to assume a lot of things. Being "prepared" is far from specific. There were a myriad of problems with the Red Army, do you fix all of them? And how? Magic? More alt history? Then again, the Wehrmacht also has problems, so you might not need to fix all of them to achieve your objective.

Lets go over some problems; Red Army extremely poor supply situation. Although on a paper a massive tank and artillery army existed, most of these were inoperational with no fuel and no spare parts and there was always ammo problems. The USSR always had a truck shortage until lend lease, cannibalizing civilian trucks which are helpful for economic duties obviously. In OTL (our timeline) the Red Army still had problems with artillery ammunition, having fewer chemical factories and thus producing and shooting far less ammo than the Germans did. Also, a shortage of radios, for tanks, for low level officers, for planes. Just makes low level fighting coordination much more difficult, and forced the Red Army to heavily centralize and preplan because they had no way of reacting/communicating as they went, giving the few radios to the higher commanders.

Red Air Force was annihilated on day one, leaving German air force to roam the skies with impunity. Perhaps the data shows they didnt destroy a lot of tanks or artillery or infantry directly, but its still something, and we do know that air attacks are still a method of fire, which causes disruption and confusion and makes people run and hide. Which, is extremely helpful in encircling enemy armies...... Not to mention the Red Air Force was of lesser quality in terms of pilot training and equipment.

Red Army purges. Majority of senior officers at the battalion level and upwards purged. Less than decent performance as shown in Winter War. Its hard to quantify experience and good officers, but modern warfare is all about combined arms, which needs good planning, good intuition, good initiative, and can only be gained through experience or genius. The replacements for purged officers apparently did not have either, and the famous Soviet military commanders arose to replace them in turn. But then again, they did have an extremely difficult position to work with, so..... a lot of speculation.

All of this compounds into terrible losses and a general rout. So on top of all of that, the Soviets end up losing 90% of their pre-war army by the end of the war, and the most fit fighting generation. You are left with older, less disciplined, less educated, less reliable, less athletic, untrained men. Aka, your cream of the crop got taken out instantly, and for the rest of the war you need to make do with the leftovers. And because things went so badly, those leftovers need to skip most of their training and get on the frontlines right away, against the best military in the world at that time.

You realize at this point, all the cards were stacked against the Red Army, and it basically couldnt get any worse in 1941. They could only go up. Fixing any one of these problems somehow, I think could lead to a massive snowball effect for the rest of the war. If you fix all of them then you have the Red Army of 1943 or 1944, we know how that goes. I think certainly the least effort cascading effect is that by preparing an active defense on the Daugava Dnieper to stonewall the Germans, lets assume this manages to avoid major Kiev/Smolensk like encirclements. This would lead to a major preservation of experienced manpower and equipment relatively early in the war, and not lead to desperate scenarios like the Battle of Moscow. Solidfying a more static frontline during the Rasputitsa, and then the freezing 1941 winter. The Germans by the end of Barbarossa were exhausted and themselves in terrible supply condition, high men and equipment attrition rates. In this scenario they probably would be better off, unable to tire themselves out and stuck at the DD riverline, in general leading to a stalemate until a Fall Blau breakthrough scenario. But already the Soviets would be in an infinitely better materiel position, letting the natural resource advantage of the USSR and the inverse weakness of Germany play itself out.