So lemme see if I have this right..
The timeline is unaffected, it merely affects alternate timelines in which they travel to, which was fine because they only needed to borrow the stones. Then they planned on returning the stones to the exact point in those timelines to prevent chaos ensuing in those realities. Loki teleported away, but this won't affect the timeline we know, since everything we know has already happened and cannot be changed. I imagine this Loki will be the one in the Disney+ series, and not the one we grew to know.
It seems the majority of Spider-man's friends got really unlucky and "snapped" because in Far From Home, they're all relatively the same in age. Apparently Aunt May did not get dusted, and so it seems odd that she's fine with Peter just going on a trip halfway across the world. This makes me think that while the beginning of the next movie might be "minutes" after Endgame, we will see a slight time jump after the initial exposition.
Seeing Thor fat and bearded was super surreal. Seeing him join the Guardians of the Galaxy was perfect. I do hope he ends up in Guardians 3, but only time will tell. He and Rocket have excellent chemistry. I am confused about Gamora however. Did the 2014 Gamora who came through time get dusted when Thanos did? Quill said he was going to look for his Gamora, not her. And Adam Warlock is rumored for the next film, and he could help with that. Obviously if they can save her from the Soul Realm, we might get an odd end credits scene where they find Black Widow as a stowaway or something on their ship after. Either way, if you save Gamora, you can save Black Widow.. the tricky thing being that Black Widow died in another timeline reality. But maybe the soul realm is connected through all realities, not just the one they die in, so who knows?
The ending of the film was pretty awesome, and I am sad about what happened to Tony, but it's unlikely we'll see him again. After all, Thanos destroyed the stones in the original timeline. And they were supposed to send the stones they took back to the timelines they retrieved them from, leaving no stones in the original timeline. Meaning Doctor Strange will not have a time stone in DS2. Obviously anyone with Pym technology could go into an alternate timeline and steal more stones, but it would seem odd to use that plot point in this universe of movies twice.
I do hope we get to see more of Professor Hulk, maybe as a mentor to Amadeus Cho, who also became The Hulk in the comic books. It's possible that the kid from Iron Man 3 might take on the mantle of Iron Man in a future film.. he did return for the funeral. I'm thinking they may end up finding someone to play Iron Heart instead. Possibly Shuri from Black Panther. And Cassie Lang is older now, meaning she could become her alter ego (of which she actually had a few in the comic books). Seems like they may be potentially setting up a Young Avengers film.
I do wish we got more face-time with Captain Marvel but its possible Marvel wanted to see how well her movie performed and thus didn't want her to have too much screen time if it turned out the reception wasn't that great. Seeing as how her film grossed a shitload of money, though, we'll definitely see a lot more of her in future installments. And apparently they filmed Endgame before Captain Marvel so we'll get to see her more like she was in her solo film, which I'm excited for in the future.
Now I did come up with a theory on how they might introduce the X-Men..
After they undo the Snap and 50% of universe returns, perhaps something is different. Maybe being snapped and snapped back affected their genetics, added a random gene that will be known as the mutant-x gene. Maybe it was a dormant gene, but either way it has been activated in a small percentage of the vanished, causing a small portion of them to develop special abilities.
So maybe the x-men in the MCU are just people who came back after the snap, and used to be normal. And what's interesting about this is that maybe some of the current MCU characters we know could develop these powers as well, as many of them were dusted and returned.
This is probably one of the best methods of introducing the x-men into this universe. And there is already a precedent for it. Scarlet Witch and Quick Silver got their powers from an infinity stone, albeit through human intervention.
I certainly like this idea a lot more than "oh they were here all along, we just didn't know about them" or something.