A Pricing Rule is a flexible way to add other kinds of payment scenarios to the registration process.
The standard path is for an attendee to choose a Registration Type - and then pick the Items (Options) available to that Type. Very transparent and self-selected.
Pricing rules deal with questions - which the attendee answers on their registration form - that have prices associated with them - but are more complex than a simple choice of items.
For example, you might have a question about Program Materials. Would you like to purchase Program Materials Y/N? If Y, in paper, online, DVD, or audiotape? If paper, to be collected onsite, or mailed to address? And each of these answers could have a different price associated with it.
The registration form is far more powerful at using this type of cascading logic to ask questions - than the shopping cart. So for certain types of payment areas - the Pricing Rules are a better way to go.