Doing it in engine or in after effects or flash could give you that control but the setup on that kind of thing (not to mention learning/ figuring out how to do it) is probably going to take longer than just sitting down and doing some grunt work. I would generally avoid it unless you see yourself using the technique for a LOT of animation.
Easy level would be setting up symbols/layers in flash/ae and animating them swinging once then you can just manually type in where you want animation to start and stop and move the symbols around. You can get more complicated with rigging to give it intuitive controls but that is above anything I have experience with and almost certainly not worth the time.
On the run animation I would say the general impression of it is good but there's some stuff in there that's strange, particularly I would point out the front arm jittering at the front of it's swing and the back arm popping back in front of him when his back knee is lifted. I would also watch that head movement, I get more of an impression that he's moving his head from the neck rather than it being the whole body moving up and down, I would expect the sword to more or less be covering the collar all the time since its resting on his shoulder which is moving along with the rest of the upper body.
Loving the designs overall, this skull guy lumbering along is going to be very cool