As far as the Flood is concerned, i would not want to see them back. They were a part of the original trilogy, this is a new trilogy.
Plus a large part Halo 3 is to destroy the Flood for good. If they can survive the firing of the Halo array, the destruction of instillation 04 and 04B alongside parts of the Ark. Are the unstoppable???
I do like Fred's idea though
As far as the Arbiter returning though, it is a must for me. it has to happen. His and Master Chiefs interactions in Halo 4 were highlights for me, them fighting the Flood together back to back, the the Arbiter following Chief into High Charity, their landing on instillation 04B and nod on the Forward Unto Dawn. I think that they respect each other more than almost anyone else, Master Chief may even respect him near Spartan level. He is UNSC's biggest non human ally. Bringing him in would also add several layers to the story, even leading to and cement a permanent truce and partnership between the Covenant (or at least the Sangheili and those who would follow) and Humanity.
You can hardly imagine that the Arbiter would be able to stay away form Master Chief upon learning he is alive, knowing what he could do for the Sangheili in the civil war. I can imagine that the Arbiter would not be too surprised to see Master Chief alive either.
I am still holding hope that he will feature in Spartan Ops too before making a full return in Halo 5 and 6, especially after Dr. Halsey has come in.