(1) The out of the blue return of the previously believed to be dead Spider Clone who happened to have had an epistolary relationship with Aunt May for years.
(2) The unresolved mystery of the skeleton of another dead Spider Clone which may suggest that Ben Reilly wasn't the same clone than the one who died in the 1970s story.
(3) The revelation that Kaine is a Spider Clone failed prototype who tried to kill at the same time Spider-Man's main rogues gallery (because he is a precog and one of them might kill MJ in the future) and Ben Reilly (because he believes that Peter Parker is his clone brother and he doesn't want Ben Reilly to replace him).
(4) The mysterious come-back of the Jackal as a green werejackal without any real explanation about Miles Warren's previous Carrion experiments.
(5) The unexplained mystery of the degeneration of the Jackal's clones (a rip-off of the Blade Runner Replicants ?) whereas the cloning technology previously used by Doctor Doom, Arnim Zola & Mister Sinister worked just fine.
(6) Traveller & Scrier, two deus ex machina mystical characters who wasted their free time watching what happened to Peter Parker & Ben Reilly.
Et cetera (I am far from exhaustive).
Oh my god, it is so sad that I can still remember so much of this mess in 2017 ...
Frankly, it is obvious that it was automatic writing.
They were inventing this thriller as it went along.
They had absolutely no idea what they were doing, where they were going and how they would end this storyline.
The only thing that mattered was that the storyline was selling books at a time when the comics' decline in sales started.