No one's valuing the small tournaments more highly, they're accorded the values they have according to the ATP point system. They both have one grandslam each, but Federer has one more Masters more than Djokovic and has two other titles. Grandslams are not the only titles of the year otherwise players would not even bother playing in the other tournaments. And even if they are, they both have only one GS title each YTD. Don't know where Djokovic fans get off AS IF he beat Nadal in the RG final.
As for this year's RG final, didn't that occasion in particular close the book on Djokovic "having Nadal's number" and likewise nonsense?
He hasn't, and hasn't ever been close to his 2011 level ever since USO 2011. Sorry folks.