Another aspect would be that since you beat the champion,you should actually be the champion,yet Wallace (or whatever his name was,cant remember) still keeps his place,as with all pokemon game champions
Pokémon champions can roam about, this is proven in Gen 2 when Lance pops in here and there. There are also points in the anime that show the elite 4 and champion spending time outside the Indigo Plateau (or whatever they are called in each gen).
You probably don't get to be champion because that would be considered a job and your character is too young to have such a job. The only reason you got to challenge Blue/Gary was probably since he was already there and had just battled Lance.
This situation is particularly annoying considering that the Hoenn games are the only 3rd gen games without a Level boost from the elite 4, so you'll battle the elite 4 more often here than any other game. At least gen 2 has stronger wild Pokémon afterword.
Seeing as you're not allowed to keep the championship status and will inevitably be back to challenge them, perhaps she overheard a plot to 'end' the competition once and for all.
"Here's some advice before you face the champion... when he pulls out his last Pokemon, take note of the snipers at the South and South East corners of the room." "Could it be that it's already over... and that they've already assassinated your Pokemon?" 'Only champions can go in my foot, don't you see he's going to knock you out and kill your Pokemon?'