Comment 221 for bug 1226962

Awesome news! I found fix for this.
1) Disable of gnome control over keyboard:
gsettings set org.gnome.settings-daemon.plugins.keyboard active false
2) Set desired settings for xkb:
setxkbmap -option grp:rctrl_toggle,lv3:menu_switch us,ru,ua
You can add this to autostart
Here I switch layout with Right Control, Menu key is used for third level of keys and I use three layouts: English, Russian and Ukrainian.

One notice: keyboard indicator on panel lives in parallel reality in such setup, so I'm using gXneur to indicate current layout (only this, and disabled input monitoring, looks like gXneur is broken in Ubuntu 13.10-14.04 with GNOME and Unity) and disabled original one in keyboard settings.

As the result - I have all possible shortcuts working on any layout, switching layout with one key - right ctrl (not possible otherwise in GNOME) and separate layouts per windows and keyboard indicator with gXneur.

Yes, such ugly but perfectly working hacks because of "smart" decisions of GNOME developers.