The colors are a way to sort your player pool.
In 2.0 it provided 4 options: High, Medium, Low, Not Set.
In 3.0 you are provided with 5 options: blue, green, orange, red, and the baseball looking circle.
On the recruits' pages or near the recruits' names, click on whichever color you'd like to sort them in.
Later, an advanced search can allow you to sort via those colors.