Technically they do, as in the comics Force Works, from Iron Man season 1, was a rebranded West Coast Avengers (the rebrand was directly linked to the show). Though Force Works disbanded in season 2, and we can assume Tony subsequently formed a new team, which would be the Avengers, and they rescued Captain America from the time warp he was shown to be trapped in in Spider-Man (like how they freed him from the ice in the comics). Events are a bit out of order, but there was an "Avengers" team in the 90s Marvel cartoon universe, even if they weren't called that.
She didn't return because episodes 6 and 7 take place simultaneously - so she didn't have her powers back yet.
That change happened last week.
She didn't fly because she couldn't. The timeline isn't linear.
It's the 90s. They don't have mobile phones, and Ororo doesn't have her communicator with her. Besides which, she didn't have her powers back yet at that point. Storm did cut all ties.
You know Angel has a healing factor, right? I think it's a secondary mutation, introduced in the 2000s. In other words, he could've survived the same way Emma did.
That's a homage to the original 1992 version, which cut off to the Marvel and Saban logos before it got through all nine members.
Magneto had no funeral because he had no body... which, of course, is because he isn't dead.