Wow. Lotta thoughts here and lots to unpack. I've only watched each episode once as they've come out so I need to go back and do some rewatching deep dives for sure. I'm loving the series more and more with each episode.
A few of my thoughts as they've evolved...
There's speculation that S.W.O.R.D. may be setting up the introduction of the Fantastic Four which I find intriguing and plausible. During Monica's tour of the facility I could easily envision Reed Richards there. Also, the use of cosmic background radiation as a plot point seems like a solid comparison to the cosmic rays that gave the Fantastic Four their powers in the comics.
I still think Wanda may be key to the creation of mutantkind. Although she may call herself the Scarlet Witch, her powers aren't strictly magical in nature. They were the result of Hydra experiments using the Mind Stone of which she and Quicksilver were the only surviving successes... due to some genetic X-factor? I see Wanda as very similar to Carol Danvers in that their powers were both acquired via an interaction with an Infinity Stone (Carol the Tesseract/Space stone through the light speed engine). So, similar to Captain Marvel I think it's fair to assume that Wanda carries within her a modicum of the Mind Stone's power. If this were released in spectacular House of M style fashion, it could trigger every other person on Earth with that X-Factor to manifest their dormant mutant powers similar to how Hydra unleashed hers. There was actually a comic storyline about 6 or 7 years ago called Inhumanity with a similar plotline utilizing Inhuman genetics instead of mutant. "Terrigen mist" was released across the world which triggered dormant Inhuman cells in ordinary people who were distant descendants of the Inhumans. It basically created non-mutant mutants in the comics at a time when Disney didn't have the film rights to the X-men and were pushing the Inhumans into the MCU; and it was always my thought that they were building that idea out in the comics ahead of utilizing it in the MCU. Essentially, before the Fox acquisition I think they were planning on recreating the idea of mutants in the MCU without violating their legal obligations. Now that they have the X-Men rights back it would still be a very possible way of introducing mutantkind into the MCU via a type of Inhumanity/House of M mashup.
Back to Wanda's powers originating from the Mind Stone... I actually had to look that up since I always get the history of all the stones confused! But I was surprised that was the case and it may paint a clearer picture of what's going on. If Wanda does have some of the Mind Stone's essence still within her, then it's quite possible she could perhaps be the re-animating force behind the Vision. He may be very much "alive" but only through his connection and proximity to her. Having forgotten the specifics of Wanda's origin, I realize now she and Vision have a much deeper connection as they're both products of the Mind Stone.
So, Wanda may be a mutant enhanced with Infinity Stone "residue"... Based on the information that she most likely has a big role in the next Dr. Strange movie, clearly she will and probably currently does have ties to actual magic. Her power may always have been to tap into magic as a sort of extradimensional force, but she was never really a spellcaster or magician per se. Based on what I'm seeing, comics history, and internet speculation, my money is on Mephisto as Wanda's current "helper" and future antagonist for both her and Dr. Strange. In the comics Wanda created her children from fragments of Mephisto's soul... and I think we may find out that Faustian bargain came through to the MCU in some form. The hexagon shape of the anomaly could very well be the edges of a spell in the shape of a hexagram and establish Wanda's connection to her classic "Hex magic."