To call them ugly is very inappropriate.
One can find they are getting over-designed, one can find the proportions are getting less important than the amount of character lines, one can find than German "cleanliness" is getting lost in favour of trendy design.
But ugly, well, no, really not.
Increasing regulations (pedestrian safety in particular, but also the giant mirrors) are limiting the designer's freedom (especially at the front).
Increasing ecology pressure is putting aerodynamics even more upfront, here too giving designers less freedom.
Increasing R&D cost can come at the expense of the design department, too. And it's easier to add a line here and there to hide some weight than to create perfect proportions.
Time pressure to develop a car in less time than before means there is less time to draw a car till perfection while talking to the engineers to be sure everything's exactly as it should.
Modern machinery allows more complex shapes to be made in the metal, more freedom to the designers in modelling the basic shape the engineers have let to them. So some are doing too much, whereas 20 years ago you had to focus on proportions (the substance of the car) because you had no other way to design a car.
The market has become even more superficial than before, and the carmakers want to be seen as trendy so have to jump in the new waves...or try to create these waves. Our current culture is much more about appearance than about substance. Therefore the design of the cars are becoming superficial.
All these are generalisations, and only my thoughts.
As a MB fan, I miss the cleanliness of W126, 124 and co. I hated the roundish shapes and weird headlights of the W210 E-Class, 203 C-Class, 220 S-Class and co however.
I love the W204 C-Class, but both 221 S-Class and 212 E-Class are less convincing in my eyes. And I don't like the W207 E-Coupe or X204 GLK.
Concerning BMW... The new, F01 7-Series (that I still haven't seen IRL) is beautiful. The new Z4 is heavy and doesn't inspire me though.
Bangle 0.1 was not at all my cup of tea.
As far as Audi's concerned, the only beautiful ones are the A8 (the new one could very well change that) and the beautiful A5. The others are quite boring.
However, there are few modern german cars than can be called ugly imo. Maybe the X3, or the front of the R-Class, but that's all.