I am a pretty firm believer that Ben's return to the main Marvel U is planned and has been for a while. I think the Clone Saga mini was given the green light in order to reintroduce Ben to new readers. I think I can back up this claim with some evidence as well.
1. The biggest piece of evidence to me is the cover to the free Spider-Man: The Grim Saga #1 cover. I know we saw a version of this cover a while back in black-and-white for, but the colored version is on Marvel.com now. All the other characters on the cover are alive. So why add Ben? A dead character? There are plenty of other dead Spider-characters they could have thrown on that cover, but they didn't. They have a bunch of alive current Spider-continuity characters on there and Ben Reilly. Even Kaine is in his current "costume" not the one he wore in the 1990s.
2. In recent interviews involving the "The Grim Hunt" (the big finale to the Gauntlet) Joe Kelly claimed that the Grim Hunt is all about family and that more than just Kraven the Hunter would be returning. It is my belief that this includes Vladimir Kravinov as well. Who was murdered by? Thats right, Kaine.
3. So its clear why Kaine was brought back in the recent "Who Was Ben Reilly?" Saga. Kaine is a part of Spider-Man's "family". His direct connection to the murder of Vladimir Kravinov makes his addition totally rational, and he will most likely receive some sort of revenge for his crimes against the Kraven family.
4. To conclude, we have had two big Ben Reilly stories recently, and the return of Ben Reilly's greatest nemesis, Kaine. Coinciding with this is also the warning that dead characters will be returning, and the collection of Spider-Man's "family". Who is more family to Spider-Man than Ben Reilly? I personally can't wait for Ben's return this June and July, time will only tell if I am correct in my predictions.