Sixt is the largest rental car company in Germany and I've used them quite a bit without problems, I don't think there's anything wrong with Europcar either. An A3 pretty much is an upscale Golf, many of the parts you don't see are probably identical, so I don't think the A3 is enough of a step up to justify the price difference.

On the Sixt website it says that for regular cars, they hold twice the rental price. They specifically list to categories of luxury cars for which they hold more: http://www.sixt.de/mietservice/kaution/

For the decision between FRA and DUS, I would think it would depend on where you ulimately need to go as well as on the price and itinerary.