Here, have a picture of a confused Twilight Sparkle as a buffer before the spoiler-filled episode discussion below

Wow. Not sure what else to say, just wow.
Considering that this was three episodes in one, they did a pretty good job. I don't doubt that they were under pressure to get a marketable Twilight Sparkle alicorn ready by the end of the season, thus the rush to get through to the coronation. But the cutie mark mixup part would have been one really good episode by itself. Twilight fixing Starswirl's spell and becoming an alicorn, a good second. Twilight's reaction and the coronation the third. Twilight trying to figure out how to fly and crashing into things constantly as an optional fourth episode.
It was rushed. Of course it was. That was a hell of a lot of story to squeeze into a standard episode. But, in my opinion, every moment was amazing. Lots of songs, naturally... they could have used a few less, but songs make for good montage material, and there was no way to pack all this story in without a montage or four. The first part, the mixed up cutie marks and such, was really awesome, and also vaguely horrifying in lots of little ways... Equestrian residents seem prone to getting mind-screwed on a regular basis. Also, Dash in a pot with lots of little animals with forks and knives?! Yeek! But the resolution of that first part gave me the warm-and-fuzzies, so I'm not going to worry too much about that.
As for the rest... So, apparently, Starswirl was researching a spell to make regular ponies, or maybe just unicorns, into alicorns. Would that spell work on others, with the requisite magical strength? Might explain why it was called the "alicorn amulet" that Trixie was wearing. Still have no idea where Cadence came from, or if there are other Princesses or Princes out there... maybe we'll find out more next season. But I don't think that Cadence was a result of this same spell. Celestia's dialogue seemed to indicate that nopony had ever successfully cast it before.
Too many unanswered questions to list right now. Is Twilight staying in Ponyville? How will the population react to her? Is she going to have new royal duties? Did she get a power-up, or just wings? That, and a few dozen other questions that I keep thinking of will hopefully start being answered next season.
Now for my reaction as a fanfic writer... I may write Princess Twilight stories in the future, or I may choose unicorn Twilight. Depends on the story, I suppose. But I'll probably leave Princess Twilight alone until I see how things go next season. I feel a little bad for anyone who's written an "Ascended Twilight" fic, now that it's been done in canon, but this is the risk we writers take when working with someone else's world.
As for how this is going to impact the future of Sunflower, the answer currently is "not at all". I think I'll just quietly ignore Princess Twilight for now, at least until/unless I figure out a way to work all that in. Until then, it's just going to have to be an alternate continuity.
Now to talk as a fan, and not a writer... I always knew Twilight was special! You go, girl! But I'm surprised, because when I heard about this, I was thinking that they'd have "alicorn mode" Twilight be some sort of power up that she could do when the situation demanded it, and she'd poof back to being regular old unicorn Twilight at the end of the episode. Instead, they went with full-time alicorn Twilight. Risky. Audacious. Brave and reckless. And sure to piss off a lot of fans. Not me, though. I still loves ya, Twi!