I just purchased S3D yesterday night so I haven't spent too much time with it, but I have already identified several issues that definitely need improvement.
Before I describe the issues I have to say that you are doing a great work, but you still need a very long way to justify the $$$ you are charging for this software.
Several of the issues come up while I was trying to do something that, to be honest, it is only possible with S3D so far, so I give credit for that.
So here is the scenario:
I arranged several print temperature calibration pieces (http://www.thingiverse.com/thing:35088) around the bed in a way to print them separately using different temperature for each piece. I arranged them in a way so that the printer head will be able to move around without colliding to the already printed one. I prepared the processes and assigned the objects exactly in the sequence the objects have to be printed (6 processes in total).
After generating the g-code in sequential mode I went to examine the g-code... The result was disappointing.
So here are the issues which I consider bugs:
1. S3D decided to print the objects in a sequence based to an unknown logic. The sequence should definitely be according to the process sequence as entered. They are processes and have to be executed sequentially the way they are created, not in a way the software decides.
2. After each process is finished the next one changes the temperature with a M104 command instead of a M109 as I have specified in the process.
And some issues which are related to missing features:
1. There should be a way to auto arrange objects according to spacing/radius
2. A way to select all objects together and move them
3. Selecting a process at the left panel should show which objects are linked/selected on it
4. A way to slow down the outer most perimeter (I know that there is one option but it is for all of them, I am talking about the outer most)