Pylint gives very detailed reports of your code. It even provides ASCII tables with detailed statistics about the results. Data for the previous and current code execution is also available with the difference, allowing you to easily see the progress that you have made.
Because it looks for errors from a small group of possible mistakes, pyflakes is very fast. When dealing with many lines of code this is a very useful feature. When used in conjunction with an IDE, it checks the code as it's being edited.
Pyflakes only checks for names that are defined but never used or names that are redefined without being used. It also does not have command line options that offer a degree of control for the tests that you are running.