The negative comments here about diagramming and avoiding over thinking things are spot on IMHO. Planning and over thinking most often lead to trying to achieve things you are simply incapable of. You wind of conceiving of things and wrapping your mind around the problems in a way that is opposite from how they are actually solved, and so when you finally set out to solve them you either give up or throw the plans out and do it the right way.

Software development is fundamentally a messy process so the best way to start a project is to just start it, rather than wasting time planning. Having some sketches about how you want things to look, and notes about the main goals you are trying to achieve is fine; I do that all the time, but I don't regard them as concrete. The steps to get from point A to point Z are often a mystery though, and they're best worked out "on the fly". Usually starting somewhere in the middle, where the most interesting part is, makes the most sense and gets the project rolling quickly.

For instance, for this project, you might know that you will have a menu at the beginning to select options and at the end you might have a save screen or something. In the middle is the meat of the project, and the interesting part, which is looking at and manipulating/animating 2D characters. Therefore, I would start with the animated 2D characters.

Are they going to have multiple parts tied together and animated something like South Park characters? Okay, then skip down to the more fundamental aspect of that by learning how to draw one body part on screen on a plain colored background. Once you can draw the body part, then learn how to move it. Once you can move it, then add another body part and tie it to the first and move them together. Once you have achieved this, then you will have a pretty good idea of what kinds of challenges you face. At this point you can either abandon the project as being too complex, or you will have a clear idea of some next steps to take, such as adding user interface elements to control the body parts.