We don't know that for sure. They could very well never remake Gen 3 or any other game again. They worked Groudon, Kyogre and Rayquaza into HG/SS by introducing the orbs. They could just do something similar in future titles.
As much as I would enjoy another run through Hoenn, it isn't guaranteed to happen. I do think that Hoenn still has a chance of being remade in the future, but just how long should we expect GameFreak to keep remaking old games? If they remake Gen 3 in Gen 5, would they remake Gen 1 as well? If not in Gen 5, then when because FireRed and LeafGreen will be out of date as well. Would they be remade again in Gen 7?
See? Honestly, I hope they drop the remake gimmick, at least for a while. I feel like we shouldn't be expecting remakes. They should be surprises that come out of the blue!