Using the word 'never' sort of sets yourself up for defeat.
Just to name a few recent ones: Ben 10, W.I.T.C.H., Avatar, Static Shock, Jackie Chan Adventures, Xiaolin Showdown, and quite a few other shows have the 'origin' episode as the first episode of the show. X-Men Evolution also did, from what I recall. You could say TMNT 2K3 did since it starts at the beginning of them first venturing up to the surface world (even if we don't see them get covered in ooze as baby turtles until later)
In the case of DC/Marvel stuff, I'd say it's because 1) most of them have loose continuity, so story isn't important to them, and 2) everyone and their mother knows how Batman/Spider-Man came to be considering how many time's we've seen it in books, movies, comics, shows, and so forth.