I've noticed a significant difference in raft quality between MakerBot Print/Desktop and Simplify3D.
The main difference is that when MB software is printing a raft, the interface layers cross over each other (perpendicular), and the first layer of a part is perpendicular to the last printed raft layer.
Simplify3D rafts print in one direction, and then when printing the first layer, print the sparse infill parallel to the last Raft Layer.
I know that MB is not a very positively reviewed company, but right now, I'm stuck using their software because of the superior rafts. (Both in ease of removal, and effect on first layer.