Okay, here's my proposed storyline for the next six months (or maybe longer, who knows). I'm avoiding the who's gone list because well, I just don't like them (too morbid for me), but I do know that cuts would have to be made.
Anyway, if I could write the show (and was a better writer), I would have a series of scenes where somebody is watching EJ and Johnny, Bo, Hope, and Ciara, and Steve and Kayla and Joe. I wouldn't stretch it out too long, just enough to set the scene that there's trouble brewing. Then I would conveniently have Caroline babysitting all three kids one day. Somebody (masked figures of course), comes in and ties up Caroline (maybe even hurts, but not kills her), and takes the kids. A note is left that simply says "Your children for mine."
After a (hopefully very short) freakout period, the parents have to get together to figure out what it means. They gradually realize that the only connection is through Stefano -- he is Johnny's grandfather and both Hope and Steve spent time under Stefano's control. They all start digging into Stefano's past during Hope and Steve's missing years and uncover information indicating that Stefano may have used Hope and Steve to destroy a rival family. They confront him, he denies but after an impassioned plea about Johnny, finally reveals the truth -- he used Hope to infiltrate the rival's compound and Steve was part of the assassination team. The entire family was killed.
In the meantime, Stephanie and Philip are slowly (emphasis on slowly) growing closer and when her brother is kidnapped, Philip decides to use the Kiriakis resources to try and help. In the course of his investigation, he discovers that Victor was involved in business with Stefano during those "missing years" and may have known that Hope and/or Steve were alive. However, revealing that information would have compromised the Kiriakis business so he remained silent. Victor also knows something about the rival who has targeted the DiMera/Brady/Johnson families, but revealing that information would reveal his earlier culpability, so he is torn about what to do. In usual Victor fashion, he goes his own way to try and get the kids back. Philip finds out and is also torn between loyalty to his father and wanting to help Stephanie.
Also in the meantime, Sami finds out what is going on. One way or another, the WPP storyline is wrapped up and, after giving birth and hiding the child (knowing he/she is in even more danger after what happened with Johnny), she returns to Salem. She and EJ bond over their fear for Johnny, leaving Nicole feeling left out (I'm ditching any kind of baby switch story -- she just tells EJ and they deal with it). So, she starts drinking again, but Brady is there to help her and they bond further. Rafe returns to the FBI, but he knows Sami's secret so they have a bond of sorts as well.
Eventually (and not in a long, painfully drawn out way), the various threads come together and the families figure out where the kids are being held, right about the same time Victor and Philip do. Everybody heads to that place and the big showdown takes place. After all is said and done, the rival is vanquished, Stefano is killed, and the kids are saved and everybody returns home.
Then the fallout occurs. Steve deals with the things he did as a DiMera soldier (maybe a PTSD type storyline), Hope has some similar issues and they turn to each other (not in a romantic way), leaving Bo and Kayla feeling left out and a bit useless. This gives each couple some issues to work through (as B or C storylines) for the next few weeks/months. Just as things are getting back to normal, a colleague from Kayla's time in LA arrives, seeking input on a project they worked on together. Is the colleague a good guy? Is the project dangerous?
Somewhere in the course of all of this, the fact that Victor knew about Hope and Steve is revealed and there is fallout for the entire Brady family (Victor/Caroline, Bo/Victor, Chelsea/Victor), as well as Philip and Stephanie. That storyline plays out over the next few months. Philip and Stephanie get an old-fashioned romantic buildup. The conflict between their families continues to be a problem, but they gradually figure out how to deal with it. But, will something else come between them?
The fallout continues for EJ/Sami/Nicole/Brady. Part of that fallout is EJ discoverying that Sami had his child and hid it from him. Does that destroy EJ and Sami completely? Has Nicole fallen for Brady? There are various ways to play it and I'm not sure which way I would choose just yet, but it's there. Plus, EJ has to make a choice about the DiMera legacy. He almost lost his son because of it. Does he really want it that badly? Could he take it over without losing his soul (assuming you believe he has one) in the process?
There would be some other storylines going on at the same time -- Abe/Lexie/Theo, Chelsea/Nick (she helps him through his breakdown), Max/somebody who is not his niece. The main storyline also affects each of these characters, just less directly.
So, that's my idea. I know that not everybody is going to like it, but please don't hurt me. :)