spider-cides dead. kaine's around. probably has pete and Mjs baby so that's another can o' worms, so he won't be back for a while. Plus he only liked pete cos he thought he was the clone and was living the life he didn't get a chance to. So now it's known pete's the real deal what's he gonna think??He probs thinks "lets keep this baby for myself and have my own family"
Ben Reilly is dead. He'll never be back. Maybe one day a what if? might feature him or a fanboy on marvel team-up might have a flashback.
I, personally, would create a 4-issue story arc. If you've ever read "Forever" arc in Brian Michael Bendis' Powers comic its very similar to that. You'd follow a villain as he is involved with the Parker line through time:
so he'd fight Pete's secret agent parents
He'd fight Pete in his early career (under some guise) but be foiled.
And he'd fight and beat Ben Reilly years later (and far more powerful), almost killing him but stopping when he realised he was a fake. (Being powerful) he'd erase ben's memory and disappear.
Then the last ish would be in modern times and he'd confront spidey and you'd see the real deal beat him after 2-issue big fight. The villain would mention "the imposter" and so Ben Reilly would be back on Pete's mind. Cue a return to the Daily Grind and Ben's old supporting cast returns
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--A bit of Ben Reilly in Pete's life, therefore.
-- A bit of Untold Tales of Spider-Man,but without major retcons or repercussions to piss people off
-- Pete would discover more about his parents heritage
-- An original spider-man arc! i thought it was a good idea, at least