I made the same decision you did a little over a year ago. I was to the point that I really wanted to shift towards 2 rail O, but found that for my personal preferences, it simply consumed too much space. I've found that S is just about 30% - 33% smaller and scales down pretty well. For me, this meant I could use a #8 in S, where I could only squeeze in a # 6 in O. I found this very handy for crossovers. I'm not sure everything you want to run, but I've found that about 45" - 50" radius is very comfortable for 4-8-2's and 2-10-2's with all their drivers flanged. Depending on what you want to run, I think 40" radius is about right. Keep in mind, I like broad curves also.
Here is what I can say to your questions:
1. I do not know of anyone that currently makes a TT or transfer table in S.
2. S Helper Service Freight Cars are as good or better that Atlas O, IMO.
3. Kadee couplers are available in S
4. American Models makes a Trainmaster, but I am not sure how correct it is for what
5. Shinohara makes code 100 flex track along with #6 and # 8 TO's. You can also get
just about any type of TO available from Tomalco.
Lastly, with MTH, they have pretty much said that you will not even see production samples of newly tooled SD70ACE's until late next year. IMO, sometime around spring York, you will probable see an MTH catalog with SHS F-units that have PS3 and DCC compatability.