Speaking of clones, my big thing is Ben meeting Laura (and Gabby) Kinney and them relating their own and to each other's struggles to find a sense of self and personhood. Plus, if Gabby could befriend Deadpool, I'm pretty sure Ben won't be that much of a problem for her.
Considering Mister Sinister has messed with Spider-Man in the past and encountered Ben Reilly before (see the X-Men/Spider-Man miniseries by Christos Gage, specifically #3 which took place in the 90s during Ben's time as Spider-Man, and more recently the Spider-Man and the X-Men series just prior to Secret Wars), I'd like to see something come of the Sinister Scarlet Spiders, too. More to the point, I'd like to see Ben tangle with Miss Sinister, who may or may not have a surviving Sinister Scarlet Spider (or more) under her thrall as part of her Ultimate Marauders (formerly the Ultimate X-Men).