I think it's because they just didn't really have a plan in the beginning. So, they had to retcon and make it up as they go along.
The answer to why Thanos gave Loki the Mind Stone in the Scepter is that they just didn't know that when they were making The Avengers.
I think it's cool though. I think all the new colors make more sense and fit better. My only complaint is all the physical, real-world aspects, Space, Time, and Power/Energy are all cool colors and the more metaphysical Mind, Soul, and Reality are all hot colors.