One example would be having several Arranger Rows with the same pattern but setting different lenght and/or start position. Will get you some small variations of the same pattern, instead of needing to 'program' them in other patterns. And of course, not to mention the control of how many times you may want things to get repeated.
Another example is to use the Arranger to Mute any each track whenever you want it, for building song dynamic/structure variations. But keep in mind that the Loop setting in playback-menu may lead to some unwanted sideeffects: if a track is in mute first, everything is fine. Unmute, everything is fine. But if you want the Arranger to mute again, the result depends on the Loop setting. If set to On and/or Auto it will just continue to sound, regardless of your Arranger attempts to try to mute again. Logical in a sense, but still it confuses you sometimes...
Another thing to keep in mind also is that the fader position overrides anything the Arranger does. The Arranger can let you select which patterns that will be in Scene A/B for each row, but the fader position will (in realtime) make the last call of which one you actually hear. Not only for the current pattern being played, but also for the nextcoming patterns (rows) if the fader is left untouched.
However, this fader override control can temporarily be 'neutralized' if you choose the same pattern to be in both Scene A/B. However, if you move the fader during this 'neutralized' pattern. But have not thought of what is controlled in the nextcoming rows (ie other patterns selected in Scene A/B) it might give you some unwanted/unexpected results. Due to the fact that you´ve actually forgot to place your fader in your 'start' position for that (nextcoming) row. Biggest issues regarding this IMHO, are if any of your track pitch are controlled by the fader.
Big fun to be had with the Arranger, still there is room for improvements IMHO.