I currently have both a 2009 S5 and 2011 335i convertible. Both are great cars, but I prefer driving the S5 over the 3-series. Some impressions:
1. My S5 has manual tranny and the 335i is auto - so my wife can drive it. We have the paddle shifters, which can be fun, but it's nothing like a good old fashioned 3 pedal car. In fairness my previous bimmers where all manuals (E36, E28, E21) - and they were really great to drive. The position of the Audi's brake versus throttle pedals make it more difficult to heel-and-toe than any of my old bimmers, so as long as BMW hasn't messed that up I suspect that if my 335i was a manual I would probably enjoy it as much as the Audi, maybe more. BTW - the trick to heel-and-toe in the Audi is to position your right heel directly under the throttle pedal, rather than the more natural position between the two pedals.
2. The 3-series has the damn run flats. They are noisy and harsh. In fairness the newer summer tire run flats are much better than they used to be, but the winters I have on now (Blizzaks) sound and feel like truck tires. Score one for Audi.
3. Gas mileage in the 335i is much better than the S5 - surprisingly so.
4. 3-series cars are so common that no one notices, but the S5 still attracts favorable attention.
5. The ergonomics of the Audi beat BMW hands down. MMI is better than iDrive, and I can't believe how the BMW engineers managed to make some of the switches almost impossible to see from the driver's seat - auto windshield washer button and heated steering wheel buttons in paticular. They put the master unlock button in the center of the console instead of on the driver's door - yecch. And the one cup holder is a flimsy thing that pops out of the dash into the passenger's air space.
6. Neither car comes with an oil dipstick, but at least for Audi you can buy an after-market one.