Been using S3D for a long time now. Been saying the same thing. There are plenty of threads already on the subject.
Just did another dual color print in Makerware. It worked fine. I don't even bother with S3D if I want two color/support material prints. I tried every tip/quirk/hack/suggestion for months. Every time I found cases where it just didn't work with temperature, nozzle order, or whatever. Not worth the effort when I can just use a different program.
They made a good start by adding retract distance for nozzle change events but the lack of the wiper/purge tower still results in extra wrong material all over the print.
Anyway... like I said... it's all been hashed out before on the forums but I'll
anyway just because S3D is still lacking the feature
BTW I like S3D a lot. I use it almost exclusively.. except when I need different infill settings or dual colors