I don't think Ben should ever be apart of the DC or Marvel universe, just because it was just push Ben back as to where he already is now.
Like if he was in a Justice League series, he'd be only in 2 out of every 20 episodes, if he was in anything in the Marvel TV universe, they'd only have him appear a couple times for like stuff in USM or Avengers or even the terrible Agents of Smash.
AND Ben would never have any transformation sequences, especially since Marvel isn't the type of franchise to ever show how a person transforms or how Iron Man grows his armor around him (except in the movies well respectively.)
Still, I think Ben should be his own thing or be something else, and if Ben 10 were in one of those 2, this would also infect the Secret Saturdays and Generator Rex since they did a number of crossovers and references with them.
It would be cool if there was a parallel world for Ben to ever cross with one of them, but still he shouldn't be apart of any of their universes despite how ignored and pushed back Ben would be.