Nautilus has had an overhaul, too many changes for me to list them all, but some of the more noticeable ones:
The separation of "Places" and "Bookmarks". It sounds reasonable, however you cannot modify what is in the Places menu, so even if the folder doesn't exist, you're stuck with it. I don't have a Videos folder, but I cannot remove it from the sidebar.
They've also removed the tree view from Nautilus, I used it all the time, but now it's gone. I need multiple windows to look at the contents of multiple folders at once.
I cannot make a new empty file directly inside Nautilus. I could understand if this had never existed , but not why they'd remove it now.
The App Menu, or whatever they're calling it, is confusing. Nautilus has a button on the toolbar which seems to cover half of the options, and uses the App Menu for the remaining options.
The Connect To Server dialog has been changed, for no reason as far as I can tell. It now only has a text box for entering the URI, no easy-to-use Protocol/Server/Port/Username/Password sections.
Typing to locate a file will no longer take you to that file, but instead start a search. I personally hate this, although I could understand why some may prefer this.
In terms of system configuration, they've stripped a bunch of options out, again.
I can no longer enable horizontal scrolling using my touchpad.
You can no longer select a background image which is outside of the root Pictures folder (Non-recursive). You cannot even specify a different folder.
You cannot specify the background scaling (Zoom seems to be the default, no tiling, or centering etc.)
Problems with are still around:
The printer configuration is still a disaster - they seem unable to make it work correctly with networked printers. Space in the name? You're screwed.
Still cannot easily disconnect from a wireless network (although the option is there, it's not easy: All Settings -> Network -> Wireless -> click on little arrow next to network name -> Disconnect)
Having said all of that, it's still better than Unity (IMO).