Hola Hans

We are using the subjunctive here because the speaker means "you can do whatever it is that you want to do. Either the speaker is having a dismissive attitude or he/she doesn't really know what the other person has in mind (to do). 

However, if had there been a previous conversation between the speakers about a specific thing that one of them wants to do, then the speaker would have probably used the indicative:

"Puedes hacer lo que quieres." 

Here he is talking about that specific thing that is known to him/her. 

I hope this helps,

Saludos

Inma