It hasn't been thrown out the window but it's so convoluted by retcons and writers just not remembering things correctly and things just being ignored and things just being done for lulz that it might as well have been. Marvel's sliding timeline makes things even more complicated than just canon or non-. Oh and even the non-canon stuff is canon-ish because of the multiverse, so there's that. The example I always use is Deadpool's daughter. She's decidedly in continuity in recent years but she was conceived in one of the wacky Deadpool retcon stories where he hangs out with 70's Luke Cage and Iron Fist. And it could be argued "but that's Deadpool" but in that case I'd direct you to the wiki on Wolverine or Cable or Psylocke or Moonstar or Apocalypse or, hell, nearly anyone in an X-book. There's canon, but the canon is crazy and fluid and often looks nothing like what you'd normally think of as canonical.
So if you're the type who can just read stuff you want to read and not worry too much about canon or big picture you're golden. If you're the obsessive type trying to make everything fit in nicely I feel for you, but repeat to yourself it's just a show comic, I should really just relax.