What happened in X3 is somewhat vague. Yes, Xavier thinks Cyclops is dead, but that could just be because Jean thinks he is. Cyclops could be dead, or he could have survived. I don't like the whole "Maybe she blew him into the forest thing". I'd like to have seen Emma Frost have whisked his consciousness away psychically for some purpose or...something. An X4 could deal with Cyclops/Jean and the Hellfire Club, among other storylines (Essex/Sinister).
Wanting Wolverine just to be "away" so he has a smaller role is silly and kind of lazy. Wolverine is a member of the X-Men traditionally, and there's no way he'd have just up and left the mansion after his fairly clear character development in X-MEN: THE LAST STAND.
The Cure is pretty clearly potentially temporary. Which is a great metaphor.
Velvet Onion, some of that script/plot description really sounds like wishful thinking on your part. Unless Cyclops somehow was to die onscreen and then came back in the script to...die again. If you have proof otherwise, I'd love to see it.
I wrote parts of X4 and X5 scripts a year and a half ago. X4 was basically "The hunt for Xavier, Cyclops and Jean" (Which gave Wolverine some emotional motivation) after initial incidents, with The Hellfire Club and Sinister as villains. Gambit was working for/with Essex, he hooked up with Rogue, Collossus, Iceman, and Angel got more development, as did Kitty. Storm was the leader of the gold team, Wolverine the blue team. Would have been cool.
Apocalypse would show up in X5, and this arc could easily work as the "second trilogy" in the franchise, with Magneto essentially playing a pseudo ally role with the X-Men, but having his own agendas. Sentinels could show up in some capacity, and be fully realized in X5, or X6 would be a pseudo adaption of DAYS OF FUTURE PAST/AGE OF APOCALYPSE, with Cable, etc.