I've owned 3 Audi's (A4 Convertible, A5 Convertible, Q5) + 2 BMW's (330i and an X3). My Audi's have all been excellent. Q7's are a bit quirky, and I won't own one. As for the battery under the seat, that come from VW, and was done for weight distribution.
The Audi dealerships in Houston are either awesome or crap with no in between.
As for brake jobs 2500 isn't crazy. Normal for a German car. Run about the same between BMW and AUDI. They mandate replacing rotors and pads at the same time + fluid. Nothing made in china, so your paying full euro prices. The reason your average mechanic can't do the brake job is due to the electronic parking brake and the rear brakes. Audi you need their VAGCOM software to tell the system to disengage the motor that drives the back break pads (it auto adjusts during normal wear, and moves the pads in).
If your buying German, a few things to note. Lease is probably a good option. Use it for 3 years and let it go. IF your going to buy one, usually pre-owned certified is the way to go. You can get some very low miles (under 10k), and save a wad of money. If certified they come with a very long warranty and you can also get a maintenance program. In most cases, don't keep them more than about 6 years. Maintenance post that get's expensive.
The more expensive the German car, the more expensive the maintenance. M3's. M5's, 7 series, R5,7,8's maintenance costs are sky high....