Permalinks vs. Query Strings

Right now I’m making use of the query string default setup (?cat=x, ?p=x, ?s=x, etc.) because I’m using lots of “if, else” statements using these variables to display certain things depending on the query string. I’ve seen some documentation on various WP sites that encourage people to use the Permalink structure (for search engines, easy linking, etc.) However, all my page display logic will be blown away if I go Permalink.

What are the reasons why I should go with a Permalink structure instead of the query string? Any advice would be appreciated!