While I am not a former S4 owner I did cross shop the two before deciding to go with an IS-F (hopefully picking one up this week...). When you get a chance, can you let us know a little more about your S4 experience?
As for my reasons to go with the F. Appreciation for the overall package, running costs, and reliability.
The package - while the early cars are a little stiff, I love the balance of handling, braking, and acceleration in the stock F.
Running costs: insurance is comparable; the F brakes felt better stock (probably just perception or a difference in tires on the street) and are up for track duty with a pad change; You have ~ 80 hp more with the F out of the box;
Reliability - while the IS-F isn't inexpensive to maintain, after PMing people on forums for both cars and speaking to a few local enthusiasts, I was pretty confident that the F would be less expensive to maintain over the long run.
Here are a few pluses, imho, for the S4 though. Better fuel economy, AWD, and the ability to tune the engine if you aren't worried about a warranty. Yes, Stasis will give you a warranty with their tune, but that won't cover you with a CPO car or extended warranty - I plan to keep my F beyond 60k miles.
Finally, in terms of transmissions, they are both fantastic imho. The IS-F auto is one of the best transmissions I have had the pleasure of driving around on the street. Hands down the best true automatic I have driven, and on the street I think it would perform as well or better than most DCT's. I hope to provide a review of its on track performance in the coming weeks!
The DSG in the B8 Audi's is an amazing unit, and I really enjoyed driving the S4 with it. That said, I have read about a number being replaced, and the local Audi dealers and independent mechanics here said it would be difficult to rebuild (i.e. they would only put in a new or rebuilt unit). I think there have been only one or two IS-F's with transmission problems across all of the Lexus and F forums. That is a phenomenally low rate of complaints in the internet era, and is especially impressive when you consider that people drag the IS-F with N2O, track it, and even turbo the car without a proper tune.
For any S4 fans out there I have nothing but respect for the car. If I hadn't tested a 2010 Lexus IS-F I would be driving an S4 (or a tuned Evo MR but that is another discussion for another time).