This episode can be summed up by two phrases. "Greninja spamming" and "poorly written."
The entire episode is clearly drafted around releasing Greninja. Effectively it's one last display of awesomeness before the star of Ash's Kalos Team "grexits" stage left. Evidently Greninja is too awesome to Oak. Sitting around in an old man's lodge isn't a retirement betting of the ninja frog - that's for the Buizel's, Oshawott's and Snivy's of the series. No Greninja gets to fight mutant trees. And of course we can't have such a powerhouse by Ash's side when he starts from scratch as a student in Alola now can we?
And that might have been okay if the episode had been written better. But the justification for Greninja leaving is that it needs to help Zygarde (that's right even a legendary Pokémon recognises his Ninja awesomeness) fight vines created by negative energy that for an unexplained reason only he can see - that's convenient. Worse still is the actual goodbye scene. This entire "Bond Phenomena" was supposed to be caused by the strong bond between Greninja and Ash. Olympia said that Greninja had chosen to be with Ash because it was looking for love. Yet when Zygarde gives it's request Greninja more or less goes without a backward glance. No tears, no apparent conflict, just a hug and "see ya I'm off to fight mutant trees." And Ash, who raised him from a Froakie, more or less shrugs Greninja's on the spot decision to leave off saying he understands and it's what Greninja has to do. He sobs a little, but it's noticeably less painful for him than when he threw himself onto Goodra and crying into it's shoulder.
Did they actually like each other that much at all? Greninja's release seemed to consist more or less of Greninja saying "bye Ash, I'm off to play with my cool new legendary friends and won't see you again. But it was kinda cool you like, raised me and helped me become this strong and all." Even when Greninja hugged Ash, it's lack of any emotion whatsoever made it almost cold and meaningless. Ash's speech almost made it sound like he wanted Greninja to go, or at least didn't really care if he did. Strong bond implies strong friendship, which should mean not shrugging off the fact they'll never see each other again.
Aside from that the rest of the episode is fairly poor. The return of Xerosic is so rushed and simple that it feels like a prelude to the release scene and nothing more. Xerosic acted like a caricature of an evil villain rather than an actual character, his Team Neo-Flare consisting of just himself and Malamar, his project to finish Lysander's work involved driving around in a bus collecting Zygarde cells one by one - No cores apparently and he's foiled relatively easily by Clemont avoiding being mind controlled, Greninja awesomely climbing onto his bus's wing and a short battle in which Crobat and Malamar go down easily. So much for an evil genius. His plan was worse than most of Team Rocket's schemes. Why couldn't we have had something involving Essentia and Malva like in the games.
It's not like it immediately jumped and agreed to the Zygardes' request. IMHO, it seemed a little hesitant; it was only after Ash's speech that it decided to stay to protect Kalos. Part of loving someone is knowing when it's time to let them go; and you can love someone deeply, even if you are far apart from each other. Ash said so himself; his and Greninja's bond won't be broken by distance.
That's literally what happened. Ash said Greninja what will it be, and Greninja walked over to Zygarde. Ash's speech made it seem like he was completely understanding of why Greninja wanted to leave and if anything encouraged him to do so. There was no "I'll miss you" or "I don't want you to go." And while you can love someone deeply even if you are apart, the fact remains here they're never going to see or even talk to each other again. They can still love each other, but they can never express that love or enjoy each others company, which is kind of part of loving somebody. Their connection with each other now will only exist in memory. The bond may not be broken but it doesn't really mean anything.
"The bond Ash and his Pokemon share transcends any silly goal of winning the League. In a close relationship that a Pokemon and their trainer share, we have been shown time and time again that trainers always take into consideration their Pokemon's wishes and vice versa. It's a mutual relationship of respect.
It's not so much that the wishes should not have been taken into account but the fact that they existed in the first place. Greninja literally seems to have decided on the spot, "yeah I want to go and fight mutant vines with legendaries, goodbye Ash" despite the fact that they're supposed to, as Olympia put it, love each other. It can't really be a close relationship if one partner is happy to end it to do something he only found out was a thing less than five minutes before. At least when Goodra left, a more emotional scene, it was to be with and protect friends and family it had been with long before it had met Ash and presumably had a closer relationship with and cared more for then it did with Ash. When Dustox and Butterfree left in their respective seasons it was to be with a mate and for the opportunity to start a family - that's something that the two Pokémon were probably instinct driven to do so it's understandable why those wishes exist. What is Greninja exchanging Ash and a chance to grow stronger with him for - a chance to fight vines with two Zygarde cores it had only just met to combat a threat it had only just heard about. I suppose you might leave a partner for a job or out of a sense of duty but I'd expect most people to be sad about it. Greninja brushed it off like it was nothing.
"
And I repeat, Greninja was never going to make it to Alola anyway, so I am pleased it got its own story.
The release isn't so much the issue it's the bad justification for it. Goodra left to be with friends it had before meeting Ash and to protect them, Butterfree and Dustox went to be with their mates - who they'd only just met. Could we have at least had a Greninja mate or a pond full of Froakie that needed him more than Ash. Random vines, filled with never heard of before negative energy that Greninja it just so happens is the only one who can see is poor.