A few factors. The Germans were massively better organized logistically and in terms of command structure, not to mention the commanders were simply better. However, practically, the Germans were able to move everything they needed by rail to the front and concentrate men and material where and when it was needed. The Russians could do this in some areas, but not others, and not in any kind of standardized fashion. The reason for this is, as we learn in WW2, the Germans can move anything they want east until they get to Smolensk. They never got to Smolensk in WW1. This simply shows that the Germans occupied territory as reasonably as possible, as they did not end up overextended like they did in WW2. Their occupation policies were perhaps not genocidal, but they were very harsh and brutal, however, it did not lead to guerilla action primarily because of the unpopularity of the war in Russia as time went on, as well as the lack of government initiative in forming unrest in occupied lands, many of which were not even ethnically Russian.
On a tactical level, the Russians had massive shortfalls of artillery ammunition and guns, and this showed itself to be critical, as the Germans massed artillery to great advantage. The German Army seemed to be a step ahead of the Russians more often than not on a technological level. There were more machine guns per capita among German units, with more ammunition, and the Shock tactics were used particularly in the later parts of the eastern front. Gas was first used against the Russians, and it was far more successful in the East due to a lack of Russian gas masks across the front, making the use of gas pretty damn lethal. There are also stories of Russians not having rifles to fight with, which are likely false but based off of the true notion of the poor logistical support for Russian field armies. Rifle ammunition WAS known to be an issue, particularly in the early parts of the war. Russian infantry training was insufficient compared to that of the Germans as well, but this was not nearly as critical as the inferiority of Russian Junior officers to their German counterparts. Despite all of this, however, the Russians were still better in the field against the Austro-Hungarians and Turks, so make of that what you will.
But basically, Russia was from the very start to the very end facing a far better led, supplied, trained, and armed German Army in the East. It is not really surprising that they had issues in WW1.