Several of the settings from ibus-setup have been moved to System Settings >> Text Entry, but something in this change to the backend has broken some key functionality in Ibus. Ultimately, this needs a bug report; but I haven't figured out exactly what to report just yet.

Depending on the languages you use Ibus for, you may still be able to get it to work well enough.

State of Ibus after installation

After a fresh install of 13.10, I could not add Ibus input sources in Text Entry. Moreover, although apt showed Ibus as installed (which it was), searching in the Dash showed Ibus as not installed.

Partial resolution

Reinstall Ibus: sudo apt-get install --reinstall ibus

After reinstalling Ibus and rebooting, Ibus input methods were available in Text Entry.

Some methods, such as Anthy for Japanese, seemed to integrate well with the new system. Anthy configuration settings were available from a button that appears next to the keyboard layout button when Anthy is highlighted in Text Entry. All in all, Anthy worked fine.

So depending on the language you need, you may find everything is ok after reinstalling Ibus.

Larger problems with Chinese input methods

Chinese input methods from Ibus seem to be completely broken. ibus-setup can no longer communicate properly with DConf, reporting permission problems accessing /run/user/<uid>/dconf/. The settings themselves are still available in dconf-editor, but most of them do not seem to be honored by the new backend setup and changing them had no effect. When highlighting the Chinese input methods in Text Entry, a configuration button did not appear like it did for Anthy.

As a result, it no longer seems possible to change the pinyin configuration or show the configuration menu. In it's current initial state, pinyin input offers both simplified and traditional characters for some words, but not all of them, making it impossible to type in one or the other, let alone to switch on the fly. Changing the simplified/traditional setting in dconf-editor is one of the few that worked -- but only after rebooting, which is obviously not practical.

Suggestion

I imagine these issues will be fixed in time as the bug reports start coming in, but one suggestion is to use fcitx if you need Chinese input. fcitx is used by Ubuntu Kylin. Install it, switch the default input method in System Settings >> Language Support to fcitx, and reboot. After that, configuration menus for all input methods were available again. (You don't need to uninstall Ibus if you will still use it in some cases.) Like Ibus, several fcitx input methods have separate packages, so you may want to browse the packages in Synaptic.