I would have to give it to the Imperium. As counter intuitive as it sounds, the Empire just does not have the experience waging war that the Imperium does. In the 40k Universe, the Imperium is constantly fighting. They are basically in a little environment much more chaotic than the Clone Wars nonstop. The idea of any sort of peace is totally alien to them. Additionally, in terms of sheer number of troops, instead of some sort of rigorous lifetime training routine like Stormtroopers get the Imperium tithes huge number of soldiers from it's planets. It is very likely that a Stormtrooper"s armor and weapons is better than a guardsman, but that pales in comparison to having huge number of endlessly replaceable troops. And that is in addition to the extremely well trained and well equipped space Marines, who, among many other things, can teleport into enemy spaceships, a tactic that the Empire is totally unprepared for. The imperium also has many other less conventional armies like Titan Legions and Skitarii. I could go on, but this is already getting pretty long.