It seems that vast majority of Star Wars technology was designed and built by the marketing department. Here are a few engineering suggestions that could help the bad guys win in Epsiodes -3 to 0...
1) Use firearms. Blasters are slow, not very powerful, and easily deflected by a light saber. An AK-47 would be far, far more effective. And don't forget the training! Despite the advantage in fire power, the storm troopers clearly can't shoot straight. Take them out to a range once in a while, and see how much more effective they become only after a couple training sessions!
2) If you use droids to fight your wars, build the best kind - do not waste time and money on anything else. It looks like the Destroyer model is more effective than50 units of the other kind (and even more effective than a Jedi). I doubt it could be more than 3 times more expensive. Why not just build Destroyers?
3) And while we are on this subject, let's have droids use more effective communication channels than human speech when they talk to each other. The same goes for all interfaces between the droids and everything else - spaceships, vehicles, and weapons. There is no reason while a droid should press a button to fire a weapon - a wireless interface would control it far more efficiently. Also, do invest in computerized targeting for your weapons. If your droids can already see, making them very accurate shooters is a relatively trivial task - ask any engineer.
4) Missiles seem to be an extremely effective weapon in Star Wars, except that there are very few of them. Why not build more of them and launch, say, 20 or 30 at a time? I doubt the Jedi, who have visible trouble dealing with one or two, would be able to escape ten. Also, consider building missiles that are FASTER than the star fighters they attack.
5) Consider using encryption. It looks like anyone can plug into the system anywhere and take control of everything in the space ships. This problem has been solved years ago! It really is not that hard.
6) Pack animals are slow, can't carry much, and are very, very hard to maintain. They need food, living compartments, etc. Consider eliminating them from the army in favor of mechanized transporters. Animals are not very effective in executions either - this has been proven many, many times. Instead of staging elaborate shows with giant predators that always fail to kill the prisoners, just shoot your captives, and put their heads on a stick.
7) I cannot overemphasize the importance of conventional firearms. If the probe sent to assassinate Princess Amidala had used a regular rifle instead of the poisonous centipedes, the subsequent events might have taken a very different turn. And in space, consider using nuclear weapons. The laser guns you currenlty mount on your ships are massively underpowered.
8) Did you know that space ships do not need wings to fly in space? Once you get entirely comfortable with this (yes, I do know it's extremely hard, given that they even make fying noises while moving through vacuum, but making this leap of faith might be crucial to your survival - do it!) you can start using very different design paradigms - like, for example, minimizing the surface area so your spacecraft is easier to protect and harder to target.
9) On the subject of spaceship designs - there must be something in the way you build them that makes them explode after they are hit. Unfortunately, this applies to all other vehicles as well. While this generates impressive visuals, this design point leads to unnecessary casualties among your troops. Consider enclosing whatever it is that explores in extra layers of protection. You have already solved this for your small weapons, which do not seem to have the same problem. Why not use similar design everywhere?
10) This is more of a tactical rather than an engineering advice, but I will give it anyway. Instead of deploying the Walkers and other weird ground assault vehicles, consider attacking from the air to suppress the adversary's ground troops.
Follow these simple steps, and you will be invincible - at least as long as the Good Guys(TM) are controlled by the marketing people.