After the Johto region there are a few things that you can do. However , I would recommend that you go to Hoenn and complete that region first.
To do so you will need to train a Rattata to level 80 and beat the Youngster Joey boss, at the Indigo Plateau. If that doesn't interest you then you could always visit some of the MS only maps like Sevii Islands or the Johto Exclusive maps, or you could start to progress in the Mew and Celebi quests by getting all the dex data for the first and second generation.