Check out the original 4x8 HO plan at the centre of this Ed Vondrak plan. I don't know if it's all do-able with AF track geometry, but it offers the kind of operation you might like in close to a 5 x 9 in S gauge. The original stand-alone layout had a locomotive spur at the bottom, plus there's a passing loop. The loop allows you to switch the sidings and accessories while having another train run on the outside main line.
http://www.wymann.info/Shuntin...hics/Vondrak-TPI.jpg