I had to add some price sets to our recent project and I think I managed to get both the existing system and the price set system to work side by side. To give you an idea of why I had to do it, think of this; you have a specific membership open to organisations, the amount that the organisation needs to pay to join is based on its size. A company of 2-4 people will pay less than a 300+ employee company.
How did I do it? I added a system similar (and borrowed code) from the events system. I used the custom fields and not the price sets as defined in events. When I had the prices available I had to implement a complicated radio button system (complicated in code not usability) to get the price chosen. This means that if a price set is available, it will be shown and can be selected as a sub set of the main membership options.
I guess the best thing to illustrate this may be a picture. We haven't finished the theme yet so here is a VERY small glimpse of what we have set up.