I doubt it was "discontinued" due to a lack of quality or desirability. A few years ago Taylor felt like they had become the "cutaway / electric" guitar maker, and split their line into the acoustic-electric (x12ce, x14ce, x10ce, x16ce) series and the pure acoustic (GC-x, GA-x, DN-x, GS-x) series. The acoustic series usually did not have cutaways, and sometimes no electronics (not everyone wants a "ce" model). The division appears to have diluted the brand a bit and confused things, making more model numbers for dealers to stock. Ending the pure acoustic series just makes the retail end a little simpler. You can still BTO almost anything if you object to certain features of the standard line (like cutaways or the electronics). For example, a lot of people dislike the ES system and want to put their own choice of pickup in, so they order without the "e".
It would not surprise me at all to find minor cosmetic differences between a 616 and GS6, but the two guitars should essentially be the same. The maple 600 series is the one that Taylor uses for different stain colors, so that may explain the darker wood that you saw. I have seen some with a reddish brown stain -- almost mahogany colored -- on the back & sides, even though they were clearly maple bodies.