I have compared the 009 and 009S running from the same amp (T8000) today.
The room was somewhat quiet, but I had only two source options: my iPhone (connected through Apple's lightning adapter directly to the T8000) or their CD player with their own music. Even though the listening conditions weren't ideal, I could make a rough comparison.
The 009S had a more evident bass, a fuller body and overall sounded more natural IMO. The treble on the 009 (at least out of the T8000) is a little bit annoying for me, and the 009S had this fixed (phew!). I thought it was a bit more resolving too.
I talked with Mr. Sasaki (former Stax Director and Sales Manager) who also hosted me when I visited their factory last year. He has been working there for decades now, and unfortunately has retired last month. He is a very nice and knowledgeable guy.
He said that the 009S started being developed 3-4 years ago. For its voicing, he said they used the 006t and 727A initially, and then the T8000 when it was released.
I asked about discontinuing the old 009 and he said that for now they will keep both, but depending on the sales, the 009 may fade out or get discontinued.
I also asked if the 009S is meant to be just a different flavor from the 009, or a higher level product. He said that "S" stands for "Special" and that the 009S has been developed to improve on the 009 imperfections.
This hobby is weird and some may prefer the older version, but I know which one I'm buying when my T2 arrives.
On another note, I told him about the DIY buildings of the T2 and showed some pictures of the ones made by Kerry. He was very happy and proud to know about it, and even happier and "grateful"- his words - to know that it bests every other stat amp out there.