Madrigal is gone, along with the whole evil warlord who is the new governor thing, the rubble is not part of it anymore, but we kept the main characters like Soren and his family (who I actually like quite a bit). Kwan is still here, but they have given her a purpose connecting her to the flood. I still maintain that this whole thing could have been done with Makee remaining dead. She doesn't add anything to the story in my opinion. I still think they should have left the flood until the finale of the third season (or like late 3rd season). That way they could have the realization about the flood after learning about the ring, and destruction of the flood (or at least presumed destruction) with the destruction of the first ring (like in the games). Also, they still have the opportunity, and I am going to place my bet now that season 3 finale is going to involve a warthog run along the ring as it explodes. That (hopefully) will be awesome.
Also, I will now begin morning for Kai. Not as much as I morn for Vannik, but she got a honorable death, that I thought was very fitting. I think she is actually one of the better written and acted characters. I like her "discovering her humanity" arc way more than the chief's.
All in all, I think this season has gotten really good. I hate that we had to lose the other Spartans but I feel like it was necessary to get the Chief on his solo adventure with Cortana as we know and love him. I will definitely be rewatching this season many times while I wait anxiously for season 3. Also, Paramount has a show about the popular video game ARK Survival Evolved which is very good. Anyone who likes that game should definitely give it a shot.