One thing that concerns me is who is going to be around to support and maintain those modified Audi/Mercedes engines in 40, 30 or even just 20 years? Let alone build them?
With car manufacturers' product cycles being quite a few decades shorter than the life span of a GA aircraft, isn't it rather probable to end up with lots of perfectly good aircraft with no new engines available? Especially if, as I have understood, the current breed of diesel engines (and gearboxes, and clutches, etc) are actually replaced rather than overhauled at TBO (or well before...).
Another concern, which may or may not be founded, is that the fuel economy displayed by some diesel engined aircraft is in no small measure due to a less powerful engine. Take a clean design, put a 135 hp engine in it, and say "look at our cruise speed! The ancient 180 hp spam cans don't have a chance against our fantastic diesels! Buy one you too!". Sure, but that clean design isn't nearly as helpful in a low speed climb, making both takeoff
and[*] landing performance suffer. Install a 160 hp diesel, and the fuel economy is nowhere near as good anymore. Keep the 135 hp and you can't operate out of many shorter grass fields.
Poor short-field performance in new aircraft is already a big problem IMHO; a C172S already has significantly worse landing performance than a C172N, and many people don't even know it...
With even worse performance, we will either see more landing accidents or people will eventually wake up and have to move away from most grass strips. What many also do not realise is that near sea level, on grass, with less than maximum weight, landing performance is usually limiting, especially when adding the recommended (or mandatory, where I fly!) 1.43 safety factor. Hence they don't even bother checking landing performance, assuming takeoff is more limiting. Then they run off the far end on wet grass (somone just broke our Archer II that way). But that's another story...
Add to that reliability concerns that are not just teething troubles, but fundamentally due to the fact that it is necessarily a much more complex engine with many more things that can go wrong.
It's problematic. I hope they get the diesels right, sooner rather than later, but in the meantime I expect to stick with Lycomings and Continentals
(or even Rotax... 
) for quite a while.
[*]: Less power -> less ability to climb with full flaps -> flaps can not be as draggy -> flaps most likely less effective -> higher landing speed -> longer landing distance.