Yes, there is the inconvenience of people having different ideas of what makes an optimal program. However, in the case of Gnome3, the Gnome team has been developing fallback mode, which will be used in some GNU/Linux distros in their next releases. So there is still a good deal of original functionality still in place. (And yes there are still variants like XFCE, and other alternatives.)
However, the main point isn't whether we can get as much eye-candy as humanly possible. Free software operating systems may always be lacking some set of features that are present in proprietary systems. But the real issue is how many _anti-features_ there are. We know about Apple's decision on storage policies because it is blatant and they were up-front about it. But there is so much in a proprietary program that we can't easily monitor. It may sound paranoid, but there are likely backdoors, etc. in many of our cell phones, allowing paying governments to listen to converstaions, even when it's sitting in your pocket, or it looks like it's off but still has the battery in. http://www.neatorama.com/2011/05/29/gmail-hackers-used-us-go... Gmail and others are _known_ to have backdoors to user data for governments, for example. How comfortable are you with that?
And it's not limited to backdoors and spying. Apple once installed a hardware chip in one of their computers to remove certain features and sell it at a cheaper price. Removing the chip allowed users to use those features. While we usually don't have much control at the hardware level, I personally don't want to use an operating system that is defective by design http://www.defectivebydesign.org/ , with forced obsolescence just being one example of a dirty tactic that is often used. (Get the latest phone, the previous one isn't cool anymore and the new OS works like crap on your "old" hardware!)
If it weren't for Firefox, there would hardly be any web standards to speak of, and the internet would basically cater to Microsoft Windows' Internet Explorer. Microsoft resisted the development of the internet in its current form because it allows users of virtually any operating system to use the web to its fullest potential. I don't think Apple is very much above that kind of thinking. When there weren't many apps for the iPhone, Apple touted the idea of web-based apps, because it was an easy entry point, and there weren't many binary alternatives in the "ecosystem". Once there were lots of programs in Apple's (censored) store, they began discouraging the use of web-based applications and encouraged everyone to make programs compiled for the iPhone, largely because a user of any device can use a web-based app, but you have to buy an iPhone to use the any of the programs that have been written by programmers for that device. (No cross-compiling allowed by Apple, btw.)
So whether or not we like where development is heading with a given free software project, there is a sanity to the development process in that there are no anti-features that I can really think of. If any get made, then all it takes is _one_ programmer to say, "I don't like that idea, I'll just delete that code and share the change with others, because it suits me, and because I can."
edit: spelling