Been using FL 12 for a short while now. Here are my thoughts:

• Before you could not conveniently group inserts into sub busses. Now you can do that on the fly by simply highlighting the inserts and controlling the fader, which is hella awesome. This is perhaps the only best thing about this FL update, and brings FL ever so close upto the league of Cubase and Pro Tools.
• The plugins are categorised according to type, which in my opinion makes it a bit harder to navigate because previous users have to get used to figuring out where the plugins are from the menu in the new setup...
• Before all you had to do was scan for new plugins and just tick the boxes to make them show up in the plugin menu bar. Now you have to apparently "favorite" external plugins (that are not FL) in order for them to even show up in the plugin menu. This is a pretty annoying inconvenience.
• FL Layer, which was a convenient way of saving templates of individual instruments, is hidden. You have to search for it and favorite it in order for it to show up in the plugin menu. Don't even know what Image Line was thinking here...
• There are some some shortcuts you can do with the mouse which sometimes gets in the way when editing MIDI data in the piano roll. For example sometimes when I'm moving a note it suddenly gets "muted". This is pretty annoying as then I have to delete it, create a new note and then place it again. I probably have to read up on these new shortcuts, but ain't nobody got time for that!
• I seem to be using automation a lot more in FL 12 than FL 11. Hence can't comment on whether there are any differences as it seems to work fine for me.
• Most of my plugins don't even fit properly on the screen thanks to my crappy unadjustable screen resolution. This is not FL's fault; I need to get me some dual 17 inch monitors!!
• And finally, there is still no way to fade in/fade out on the fly without having to automate the volume. Coooome ooooon Image Line! >:(