I see this has been moved to bug reports which means nothing will be done about it anytime soon. I got a refund on the faction flip and will delete that toon and all the others that are stuck. Quite frankly I still have around 30 toons, that’s enough LOL.
Experimenting I noticed this: it seems to only be happening to toons I created after the prepatch, and of course to that faction flip. I had a handful of little toons before the prepatch and they are getting the skip offered. I had not checked them yet because they are bank alts.
So any toon created since the prepatch, whether they went through the new starting zone or the original, whether they were level 1 or a “hero” class and started at 8, or whether they were an allied race starting at 10, and faction changed toons of any level (mine is max).
Only toons already existing before the prepatch are being offered the skips.
Full UI Resets never helped me in the past.
If you go through the tutorial in Orgrimmar after Exile’s Reach, you can’t skip the BFA intro.
If you skip the tutorial when you enter orgrimmar, you can skip it like usual.
To skip the Legion intro, do it up until the Broken Shore intro, leave the instance, then go back to the guy outside Orgrimmar/at the docks in Stormwind and he’ll let you skip the scenario.
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Ok, any new toon I make no matter what route I took, the new starting zone or the old, is offered the skip. None of them.
Neither the BfA nor Legion skip is offered. I did the city tutorial on a few and didn’t do it on a few that I took through Exiles Reach with the same result, no skip offered. This no skip was applied to my max level faction flipped toon also, neither the Legion nor BfA skips were offered.
And I tried that with the Legion intro, left from the Broken shore and was put back in front of the dude outside Org and all he offered was the quest to go back, NO SKIP.
That’s why this is in the bug report forum.
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Since I haven’t seen it mentioned, have you done the scenario at least once since the new leveling scheme to see if that might return functionality?
That’s about the extent of the suggestions I can think of to return that option, unfortunately.
Horde can’t skip, Alliance can skip. 
I have this same issue. I’ve done the opening Legion scenario at least once on each faction, and have skipped it for every alt afterwards. However, after the patch, there was no skip option available for my Orc (others in my raid said they had the same problem), but my Kul Tiran was able to skip with no problem.
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Oh yeah I did them both back when the expansions released. I hate them both so much that I’ll delete the toons before I do them again. The Ally side for BfA isn’t as bad as it’s rather quick but the Horde side one is a massively unfun pain in the butt dragged out bit of nonsense.
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I was able to skip BFA intro on every new toon, you need to talk to Nathanos after getting the quest to do Stormwind extraction (dont need to do it). He should have the skip there.
I was able to skip legion intro by going into the scenario and then leaving then talking to the npc who gave u the legion intro quest and he had the skip to go straight to Dalaran [Horde]. (that one was tricky). I havent tried this on alliance side on the PTR at least, had the option to skip right from the quest giver without having to go into the scenario at all.
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OMG do none of you READ? They. Do. Not. Offer. The. Skip. That’s why this is in the bug report forum now. Apparently it offers the skip for some and not for others.
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Fun Fact: People offer solutions in a Bug Report Forum, on the off chance they work.
Stop. Being. So. Hostile.
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On my new alliance toon the BFA intro was blacked out, though i was able to skip it. Its not the only intro to give me issues since the patch either.
READ the thread first then. All of the suggestions were already covered several times. After having to say “already tried that” for the unpteenth time my patience is gone.
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Except you LITERALLY ONLY SAY THE SKIP ISN’T OFFERED
You did not tell us you tried everything we suggested until AFTER we suggested it.
You’re being hostile to people trying to help you. I’m putting you on ignore.
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READ! OMG it was stated multiple time. Just stop, you’re embarrassing yourself now.
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I am seeing three seemingly interwoven problems lately.
All my characters have ‘forgotten’ that they have finished Normal end bosses of old raids like ICC / Ulduar / Dragon Soul… meaning this week I was unable to do any of them on Heroic for mount farm etc. I reported it of course and made a bug thread post. Also noticed a lot of people’s accounts had ‘forgotten’ they had Pet Portals for 1500 and 2000 pet unlocks… meaning they couldnt learn more pets until GMs mailed them the toys again (WHICH OMFG I CANT BELIEVE IT GMS ACTUALLY DID SOMETHING!!!)… and now the game has ‘forgotten’ when max levels have completed storylines and wont offer them the skip.
A lot of IsQuestComplete flags must be unchecked in prepatch or something… and a general observation… the game is in the buggiest state i have ever seen it.
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There is a skip, at least on the Horde side (I have not tested how to do this on the Alliance side). It’s weird, but trust me, it works.
Go to the inn and meet up with your team. Take the quest, and drop it before you pick up the potion.
Get a mage to port you to Dazar’alor.
Go down to the docks. You will see Nathanos with the same quest; do NOT pick it up. Get onto the GOLDEN SKIPPER ship to Echo Islands.
Ride the boat to Echo Islands and back.
When you return, Nathanos will offer the skip.
DO NOT ASK ME WHY THIS WORKS. It just does.
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What I do it accept the poison and when Nathanos takes you to the wyver guys, select him again, and an option will pop up allowing to to skip the the scenario.
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It isn’t working. That’s the problem, he does not offer the skip to everyone. It seems to be random.