@SoundMonkey: Actually, that's not a very realistic option. Taking a break for any show means giving up its timeslot to another. Japanese broadcast isn't like ours. They don't do reruns.
Only other option is to make something to give the source material time to get further ahead or diverge into a completely different storyline like the first FMA. [And let me tell you, I hate that latter option with a flaming passion]
What makes or breaks it is if they're being serious with it and if it meshes well with the plotline. And it helps if it helps flesh things out and not just for the main storyline. Shippuden's latest fillers *set during the war* are an excellent example of this. Fleshing out characters barely touched on in the actual source material, giving us new background stories about newly introduced ones, and even giving characters we know that did nothing in the manga version getting some limelight.
An excellent example of filler done right. If it feels like a contribution or even just feels like it's actually part of the series it's in that you would not guess filler if you didn't know it, it's successfully done its job IMO.
In Kubo's case specifically, he unfortunately did not give Pierrot many options. His pacing was very sluggish and he left zero room for them to add anything without going into a completely different storyline/universe.
As for Fairy Tail, I would like to remind some that FT got an anime adaptation fairly late into its manga run compared to most popular series. It's no real wonder they didn't get to that danger zone for a while.