I agree with @Starhawk on this one. Mechjeb would do alot of un-needed moves on any decent sized craft as it tries to dock. The biggest problem with docking yourself is having patience. I, when I started trying to dock, was always in too much of a hurry to get docked, would come in too fast and end up bouncing off, which of course would cause both craft to go randomly spinning away from each other, once I learned to take my time and also decrease the thrust settings of the RCS once you get close, so that you have greater control of finer movement, can dock first time, every time, with far less resources wasted. One of the hardest things is getting the right camera angle to make sure you are lined up properly. There are of course mods to allow you to see from docking ports point of view. But you can also add a very small part in the right place and click aim camera on it so that you can put your view point where it is the easiest to see.