Why? Because we don't need training wheels any more.
Continuing the web analogy, back in the 1990s, we needed blue or purple permanently underlined text to indicate a link. Now we are more sophisticated and don't need to have it spelled out in the same way on every page. As a result designers have more scope for making pages look attractive. On occasions when you find a page that hasn't been updated since the 1990s, it's horrendously ugly.
On native UIs, it used to be the case that every toolbar icon had it's own box, to show that it was clickable button. But that was abandoned more than a decade ago, with no loss. No one wants that anymore. Here's reminders of button toolbars:
You see it's been a long time since every clickable thing in a UI needed to be dressed up as a button. Yosemite is just another step towards a less fussy UI that accentuates the content rather than unnecessary chrome.
As to the save icon, I have't see a floppy disk icon for years. Not because it's been replaced by a different icon, but because on a modern OS it shouldn't be necessary for the user to initiate saving their data, other than the first time to give it a name. Closing a window autosaves, prompting for a filename if it doesn't already have one. And autosaves happen periodically inbetween times.
If you think UIs should stop, where do you think? Some people (particulary Linux fans) think they should have stopped at CLIs. Do you think they should have stopped at Mac OS 9? Windows 95? What makes you think that the UI as of 6 months ago was the perfect place to stop?
The reality is most people are a bit reactionary. They don't like change when it happens. But once they get used to the change, they look back at the old thing they wanted to keep, and realise it was worse.
At some point, I predict that someone high enough in the food chain is going to realize that the emperor has no clothes, and people actually like shine, gloss, transparency, gradients, and color schemes other than white on white (Apple) or kindergarten construction paper (Microsoft), and we'll see a return to those types of design elements.
Actually Yosemite introduces some transparency that wasn't there before. That is a mistake, and I predict that will disappear, along with all the other cheap embellishments you list. Part of the reason they were there is that gradients and shadows can pimp up relatively low resolution displays. The eye doesn't pick out jaggies so much if you blend colors. With new retina displays, beautiful design can come with accurate hard edges, both in typography and in graphical elements.
You seem to think it's just a matter of fashion. For sure there's some fashion in there, but there are other more real motivations that guide where that fashion goes. And there's no reason for it to go back to novelty lickable items and pseudo 3D.