*Indigo Elite Four (or Indigo League). I apologize for the correction, but it really cringes me when I see the term 'Johto Elite Four' that's one of my PokePetpeeves.
And on the topic. We need a separate league OR either have only one league for all the core games, while making the familiar cities like Virdian inaccessible (You know, lame excuses like landslide or volcano eruption).
The reasons for lacking a separate league for Johto is most likely the memory capacity. Just look at what happened to Pewter Museum, Safari, disappearance of Cinnabar Island and the shrunken size of Celadon. I always imagine that, if they were to make a league for Johto, it should be located on top of Mt. Silver with Mt. Silver acting as the region's Victory Road (with more complicated puzzles of course). An another possible location is the west of Cianwood, which is later turned into a Safari in HGSS.