I had asked this same question here a few months ago, but then I recieved my answer. During Ash and Co. travels in Hoenn they encounted the Trick Master's house. This aired with Jigglypuff and a Whismur. At the end, seeing as Whismur never fell asleep to any of Jigglypuff's songs, Jigglypuff ended up staying with Whismur. So, the writers took the pink puff out of the show after finding its true friend for so many seasons.
I don't think it was a terrible way to end Jigglypuff's travel with Ash through the future seasons, however it is sometimes sad not seeing it interfere with any plans in a few of the episodes. This was also a beneficial way of ending its journey, because it at least shows it was never forgotten as Pokémon may sometimes have a tendency never to show something again, leaving the viewers wondering where it might have gone off to.