I really liked the concept of puzzles within puzzles introduced by the indigo blocks. I might make those indigo blocks different colors/designs when the puzzle types changed. For example, solving the indigo puzzle makes it totally disappear in one level, but in the next level rearranging the blocks in the indigo level makes them appear that way in the meta-level. Since these indigo blocks function in two different ways, it might be helpful for them to have a different visual design and/or different names.
As other reviewers have said, I really like how you keep building on the basic premise and steadily add new mechanics. Fun game!