I have been using simplify3d for a little while now. For the most part, really liking it.
One thing I think would make this tool a little better - the ability to have a higher level job consisting of X parts. Load the parts, then have some automation/option to break a job up in to multiple plates and slice/save gcode ( maybe ). This would be even better for things like knowing in advance you want to do something like a scale change on all parts though I'm not sure how common that is ( I'm printing something which is 2 plates scaled to 50%, total of 10 stl files )
I end up doing a bunch of this manually - having a workflow would be kinda nice IMO.