No the Brute Force and Covenant Prophet are both new covenant species, as well as there are other new species of aliens that we will see it said, so dont worry.
As well as are good old friends the Flood will be back.
So take a look at the first page to read what I posted about some new features.
An update though is information from the magazine did say that the story will not all take place on earth we will be on a space station, on a moon(possibly earth's, maybe not) full of low gravity, and buggy type vehicles, as well as some others, with Earth of course too, and a suprise.
Semi Spoiler
Towards the end it says you will go to the covenant home world, in which you will learn the truth of why they are trying to wipe out the human race, not just for a holy war, but more sinister plans. and also it says that there will be a gigantic final battle on the Covie home world, and that it will finally resolve, and bring a partial closure to things in the halo saga, and also that throughout playing halo 2 you may want to go back and play halo 1 to notice some of the markings and symbols and things that will now be explained in halo2 thats all for now, when I find more info Ill post again.
-Al the Vykker