It is complicated for sure, and it took me some time to get my head around it. But it seems to me that the complications arose because of compromises needed to be done to get this passed. Also, the current dispensation is to make it simpler over time.
This GST was probably what was possible right now and full marks to the govt. for getting it done. They made compromises which will nullify immediate gains, but at the same time made sure that the structure is put in place to get full benefits over time.
That being said, even in the current form it seems to be a huge jump from what we had.