Well the knees arent exactly perfect, when you rotate them, they twist on themselves. Try and keep the back rigid. Think of the bones as pivot points, right now you added influence from the tibia too high up the thigh, keep the verts locked to the upper leg until they reach the pivot point (in this case the tibia)...im sure it doesnt make any sense. I suggest you check the skin modifier tutorial again, see how i handle the ankle joint (you'll notice i keep the shared weights around the pivot area).
You got some verts that arent welded/weighted together, when you rotate the lower lumbar you'll see the flap mesh stuck in place and create a hole in front view.
The hands you imported arent positioned correctly, i merged kyle's on top and yours are too low.
Remember that attaching the hands deal? well you need to do the same with the cape, the pivot point is messed up too.
btw, i'm probably the one that did the rig on the malak model you are using XD.