Since your car is a 2012 model, it was definitely covered by the Dieselgate settlement. Do you know if the exhaust repairs were done on that car? If so, is the extended warranty still in effect, or has it expired by now? If your warranty has expired, you may consider deleting all the exhaust doohickies and get Malone tune done. There is certain percentage of TDI owners on this forum who opted to have their vehicles "repaired" under the terms of the Dieselgate, collected the $5,000 incentive, and then within a few days spent about $2,000 of the incentive to delete and tune their rides.
I personally never underwent this process as I sold my Jetta back (I felt that this was the best option for me), so I cannot offer first-hand experience with this modification, but long before the Dieselgate blew up, I was determined not to spend a penny on repairs of the exhaust system once the DPF cracks (and I knew it would crack one day), and, instead, go for the tune.
The day never came, so I was spared all the trouble, but if you talk to people who had the tune done, majority are happy with it. Even those who only had Stage 1 done are reporting noticeable improvement in power and torque. This is due to the fact that with Stage 1, although you only disable all the sensors on the exhaust system, you also remove all the exhaust restrictions, so the engine no longer has to work so hard, and the result is more power, more torque, and, better fuel economy. There is plenty of info on this forum regarding the Malone tune and the various levels they offer, or you can go directly to them and ask any questions you may have.
Oh, and regarding the reliability - deleting the EGR, the DPF and all the associated sensors will, in my humble opinion, improve reliability of the vehicle. The reason is simple: in case of the EGR, all the nasty stuff that your engine generates is sent down the exhaust pipe, rather than rerouted back into the intake manifold, where it forms heavy deposits that will eventually impair normal function of the engine. In case of the DPF, it is an expensive component that seems to be failing quite often in those vehicles that had the VW fix done. Removing it and replacing it with a piece of stainless pipe means that this component can never fail again simply because it is not a part of the vehicle any more. And yes, all these modifications are illegal if you plan on driving the vehicle on public roads, but I am certain you already know that. On the other hand, none of the VW executives ever lost any sleep over selling millions of jinxed cars, so why should you?