Quote: And it also can't work if we take into account the Gwen clone, because the GC would have been pregnant as well.
I'm not following you here. I mean, the Jackal's technology was all "comic book science" anyway, so the writers could have said "oh yeah, the Gwen clone was pregnant, too" if they wanted to, but I don't see why they would have to or why it creates some logical flaw if they don't.
If Jackal cloning is anything like real world science, it simply places the DNA into a new empty egg. If the Jackal took a normal human being, chopped off its left arm, and then cloned the one-armed subject, the clone would have two arms, not one, because having your arm chopped off doesn't rewrite your DNA. Nor does pregnancy.
Presumably the Spider-clones all had superpowers because the radioactive spider bite altered Peter's DNA. And yes, you could say that bearing the Osborn twins somehow changed Gwen's DNA, but there's no evidence that this "must" be the case. We haven't seen any evidence that MJ's DNA was altered by bearing baby May.
(And of course, even the above discussion isn't necessary unless we know for certain that the Gwen clone was made from a post-conception sample of Gwen. I'm not clear on the timing there, so I'll assume that was clearly established to be the case.)
Anyway, all of that is not to defend the actual storyline.