The best waterproof backpack cover will protect both sides of your pack. Many people forget the side of the pack where the harness is attached. This is where the straps and padding are exposed. People forget that water will run down the back of their hood and raincoat. While the straps will not absorb much water the padding will. This can add a few pounds to your pack.
Your backpack cover should be an addition or a continuance of your personal rain gear complete with it's own hood for your head. While your rain coat should have a hood for when you are not wearing your pack, your pack fly should have a means to protect the underside of your pack.
The pack cover should go as far as possible around your pack without interfering with the straps. If the cover did completely surround your pack you would have to undo the straps and feed them through openings in the cover to put on and remove the cover. The harness straps would prevent the rain cover from completely surrounding the pack.
The material of the rain cover or fly should be waterproof not just water repellent. Much like the fly on your tent, it should have a rubberized or plastic membrane. The membrane can be on the inside to protect the coating from abrasion and tears from brush and branches. More expensive covers have a rubber coating between two layers of nylon or polyester to protect the waterproof membrane on both sides because soft rubber can be damaged from rubbing against your pack buckles and straps.
The backpack cover should also have elastics or draw cords to tighten the cover to your pack because not all packs are the same size and have the same shape. Elastic draw cords ( dynamic ) are not as strong as static or non stretching draw cords and can be pulled off your pack if caught on a branch. But this can be a safety feature to prevent your cover from tearing when caught on branches
The pack cover should be able to stay on the pack if you decide to stop for a rest or a chance to warm up and enjoy the view. Even though you won't be able to see too far in a downpour. You should also be able to access your pack without removing the waterproof backpack cover.