I would take Thiago over Koke any day. Isco is not playing regularly as you said and Mata just transferred. I know who I'd pick if I were VdB.
His chances have indeed taken a turn for the better, once he handles himself in the cl as well as he does in the bl then theres no reason he shouldn't be on the team.
In my earlier post i forgot Cesc
I do think koke deserves a nod though him and thiago are the best young midfielders we have.