Both Team Magma and Team Aqua are done and we won't see their evil anymore, however, Team Galactic isn't officially done as what we know is that Cyrus disappeared mysteriously and the commanders were searching for him, and who knows, maybe Mars and Jupiter found him again! I am also sure that Team Rocket is going to be done this time, and hopefully, Team Galactic as well. I think that Cyrus will come back with Giovanni to rule the world they want.
I was viewing some official videos concerning HG/SS and I found that there are two additinal leaders to Team Rocket, beside the previous two. Both of them had the same appearance of Team Galactic, and one of them looked just like Mars!
I think that Team Galactic with re-appear somehow in this region, and espacially after the three dragons had appeared in this region too, which means that Johto is connected with Sinnoh as well.