Kinda weird onservation, but i seriously think pd would 'sound' different if the standard UI came with a dark background and light objects. As a few people have pointed out, the interface does have a noticable influence on the user.
Also, the default 64 sample blocksize, and the relatively expensive cpu cost of upsampling or decreasing the blocksize do have noticable impact on the fidelity.
The filters are also very rudimentary (although, the new bob~ one looks more promising). Of course it is possible to write your own with the filter primitives, but it's hard work.
Something else: being open source, means that the info and resources are put together by the community with nobody really comitted full time to the job of keeping it all together. The big commercial alternatives all have staff employed just to herd the users together and make sure their resources get shared as well as possible. Pd community is a bit stuck together with paper clips in that regard.
But on the flip side, pd's community of users is probably the single most awesome single group of people i have ever had the fortune of being a part of. Whenever you get stuck with something, there's always someone to lend a hand, and whenever you help someone else, they generally are very grateful. And the limitations of not having a huge library of readymade techno tools, is actually a real blessing. In many ways, pd inspires out of the box thinking. In many ways it's easier to set up weird interactive interfaces and algorithmic compositions than writing boring house music. Personally i would call that a plus.
Sorry, know this has gone pretty far off topic.