Well there it is - Ash has had the fight of his life and he lost. Again.
Personally I don't think this is a big deal. Ash loosing eventually is part an parcel of the anime and there's nothing wrong with it as a recycled plot line. He's easier to get behind as a protagonist when he doesn't win and it's a reasonably good message to send that he's not a sore loser. Alain as the victor I'm a little unsure about owing to the fact that he a) only entered the leauge to battle Ash (which is almost stalking behaviour), b) won the necessary badges in a very short time and c) is marked by the fact that he's still involved with Team Flare. That and he might not even have been there had Ash not mentioned the leauge to him the last time they met - I'm not sure whether it's coincident or a deliberate ironic joke but this is the second time Ash has inadvertently sealed his own fate at the leauge - he begged Nurse Joy to let Cameron register post deadline in Unova.
It's also the first time Greninja has lost a battle since I think Ash lost to Wulfric the first time and they're aren't any major battles left other than the Team Flare arch. So it's role as Ash's star Pokémon is drawing to a close. That being said it didn't have as important a role in the finals as I thought it would given the attention it recieved leading up to the leauge. In the Sawyer battle Greninja only faced Sceptile and therefore only had one win - reasonable given the two Pokémon were supposed to be rivals, though this wasn't really alluded to much. Against Alain it beat Bisharp, if for no other reason than to give it some glory before it lost to Charizard. I have to admit I'm acutally kind of relieved that if there was ever a Team of Pokémon that would win Ash the leauge it isn't going to be one with Greinja on it - It's my least favourite water starter. Maybe Ash can have something similar with Popplio in Alola. Popplio's cool.
In both battles the heavy lifting was done by Pikachu - exactly as it should be. Fighting both Sawyer and Alain Pikachu beat two of each trainers Pokémon and was only taken down by the other trainers main partner. While he hasn't had the starring role that Pikachu had in the first three gym battles, it's undeniable that Pikachu's efforts in both battles are a significant factor in Ash's success against both trainers. But that's to be expected - Pikachu's Ash's strongest and closet partner. He should play the staring role with minimal losses. This is much better than the BW series where he had far too many losses to opponets that weren't worthy of beating him - Snivy, Panpour, Excadrill and Lucario. In XY he's taken on Tyranitar and Metagross and won, and in Tyranitar's case with surprising ease.
That brings me to the biggest disappointment of this episode - Pikachu vs Charizard. Even thought it was hinted at that Pikachu might fare well against Charizard in the last episode, he lost before the title sequence. That's disappointing. However it wasn't as if Charizard dominated - Pikachu matched Dragon Claw with Iron tail but just wasn't strong enough. He still put up a good fight. And it leaves open the possibility that in a rematch Pikachu might actually win - I won't speculate on that as an Ash vs Alain rematch will probably never happen.
