I'll preface this by saying that I've always loved all of the 3A but have always held a soft spot for Anna, so I may be biased, but:
Anna deserved to win today.
None of the 3A were flawless today, so the win can't go to the one who was clean. Anna and Alena each had one fall, Anna on a quad lutz and Alena on a triple lutz. Each landed two difficult elements - Anna the 4Lz and 4F, and Alena a pair of incredible 3As. Anna backed up her skate with a 3Lz-3Lo and 3F-Eu-3S, while Alena had a (stunning) but easier 3F-3T. Both had level 3 steps with good GOE, and both have amazing spins, although Anna has more flexibility in her Biellmann and Alena more innovative positions. So, Anna wins technically for me - both with one fall, two ultra-difficult elements, and two exquisite combinations, but Anna with a harder element that she fell on.
Since both had a fall, their PCS was lower than in the past. I agree that Alena should have a higher score for skating skills, but today I think Anna was much better in interpretation and performance. That wasn't reflected in the scores. In the end, though, it's a sport, and with each skater having a fall, the one who produced the more difficult of their beautiful elements should've won. That's Anna.
It seems that Anna has to be completely clean (or have a minor error) with three quads to beat Alena with three triple axels and a mistake. That to me is critically unfair, and I think the problem stems from the SP rules. Triple axels and quads are both incredibly difficult, and yet only triple axels are allowed in the short. The reasoning for that aside, it would appear that the ISU is discouraging quads - discouraging harder elements - by having these rules and scoring Anna and Alena the way they did today. That's not progress for the sport, and it's disheartening. Fall on the second quad lutz aside, this was one of Anna's best performances (she's clearly grown into this program and it's so exciting to see!) but it seems like what she's doing isn't enough. And as a fan, it makes me upset and sad for her.
All this aside, she seems to do best when she's the underdog, so maybe this will let her go in and win Worlds decisively

.