Most of the newer embroidery thread was developed to add features or overcome difficulties that people experienced using "regular" thread. Machine embroider is not new, only the computerized parts. I've seen some wonderful work done using a Singer 15 with the feed dogs dropped - so all the movement is controlled by the operator.
A lot of choices depend on the machine and the design. If you want to do a dense design on a high speed machine, you need thread that will hold up or you'll be stopping for thread breaks and shreds a lot.
Floriani has come out with a matte finish polyester thread - it looks a lot like cotton so you get more of a vintage look without the problems associated with using cotton.