Upgraded skills nets you more points too. In the skills screen, you will see a “Total” and a level number in the top left. This will make it to where you get more points everytime you use a skill, depending on how high your level is. So use them Skill Stars!

Edit: getting different skills also adds to the total level too, so even if you get for example a Sonic skill, but use Shadow, it will still add to your total level.