I don't think it would ever happen but it would sure be amazing! Legal and properly distributed ROM hacks would do wonders for the community, think if Nintendo endorsed some of the most popular ROM hacks, potential would be huge! Plus, people often actually make better games than the main series releases haha, I haven't been the biggest player of ROM hacks, but have played through a few in my time and dabbled in advanced map etc.
It wouldn't kill the main series for me, cause it would probably be quite limited, but would really be cool to see community generated Pokemon games (for real)!