Ash-Greninja: My main issues with Ash-Greninja is pretty much anime-exclusive: it's name and it's role in the anime. For the name, really, they couldn't think of a better name for the transformed state aside Ash-Greninja like "Bond-Greninja"? As I've said before, I don't mind seeing concepts of the anime crossing to the games but direct references to main characters? Let's keep that separate. As for it's anime role, it was pretty much used because they didn't want to give Ash a Mega because he was a special anime protag snowflake. To this day I'm wondering if this was always the plan, because to me it felt like they were setting up for Ash to getting Mega Charizard Y. They brought Ash's Charizard back, it was revealed Charizard was getting two Mega Evolutions, and they introduced Alain who used Mega Charizard X and made him a rival. It felt like Ash would learn to use Mega Evolution and we'd have an awesome Mega Charizard Y vs X battle. But NOPE, as it turns out they brought Charizard back for no reason cause Ash was given a super special transformation exclusive to him cause the writers got bored making a Pokemon anime and decided they wanted to make a half shonen/half idol anime. And to rub salt in the wound, we still got a Mega Charizard Y vs X battle but it lasted all of 3 minutes with Alain & X dominating most of it.
Also I do feel this makes Greninja a bit of an odd one. The other Kalos Starters don't have this kind of transformation. Sure, Charizard got two Mega Evolutions, but Blastoise and Venusaur got a Mega Evolution and you could argue it makes sense for their to be split Charizard's Mega Evos (one kept to its original design while the other became the Dragon-type it always wanted to be); also Mewtwo got to Mega so it wasn't alone in that regard either. But Ash-Greninja is an anomaly all on it's own. Will we ever get another Pokemon with the Battle Bond power? *Looks at Ash's Rockruff with suspicion*
Blank Slate, Complex Story: I don't think there's a problem with having a blank slate character in a complex story, but the writing and gameplay has to be made around it which obviously Pokemon Sun & Moon (and apparently Fire Emblem) didn't do. I can't speak for Fire Emblem, but I can tell you where Sun & Moon fell short on this: the player's reaction. Or rather, lack of reaction. Most every scene the player has the default face while every other character is showing off various facial expressions to match what mood they're feeling. Your essentially just dragging your character around, watching a story unfold around them while having little input aside having them respond back to you in a different way (which doesn't have any lasting effect outside the scene and it all plays out the same in the end). Let's take Black & White and how it did its story. There the game made you feel important, after a few casual battles with N you were than targeted by Team Plasma as possibly the opposite opposition to N. Since the game's path was relatively linear, they were able to make set pieces to create this, let's be honest, artificial importance but make it feel it was because of your own actions of being a good trainer. You could even say the plot itself was written around that, Team Plasma wanting to release everyone's Pokemon because they think trainers treat Pokemon as slaves while your character shows N that isn't true (theoretically). But Sun & Moon isn't like that at all. The story is a personal one but not one pertaining to your character (an issue they had before in Black 2 & White 2 which was more Hugh's story your character hi-jacked). And when your character is a blank slate, this is bad because now you're being put back as a viewer of events rather then actively involved. You weren't leading the charge into Aether Paradise, Gladion was. You didn't have any major character development from your experience, Lillie did. Even Hau had more involvement and development since he failed to prevent Lillie from being taken and joined the Aether Paradise raid to both save Lillie and redeem himself. At most you were just a chaperone/bodyguard, there just to do the heavy lifting. Gladion or Hau could have easily taken the player's place when Lillie went to get back Lusamine and nothing would change.
So, now that we know what not to do with a blank slate in a complex story, what should we do? Well, how about we check other games with highly praised stories with blank slates to see what they did. Bioware games are a good example, mainly Dragon Age and Mass Effect (and there's also Bethesda's Fallout series). For all intent and purposes, the main characters are blank slates who are the driving force of the story. Throughout those games your given choice that does have an effect and comes with both benefits and consequences. This especially include character interactions where you can make it so a character deeply admires/respects you or hates you. Sometimes through direct conversation, sometimes with actions you do that doesn't match that's characters ideals. This allowed you to mold your character better, being given more speaking options and how your character responds to situations.
Now I'm not suggesting making a Pokemon game like you would a Dragon Age/Mass Effect/Fallout, I'm saying look how they did character building and adapt it. For example, have the game track how we treat our rivals and have the rivals remember and respond back in ways matching their characterization. During certain moments let us choose the way our character would act, like would we let things play out or would be intervene (and if so, when would we intervene?). This could then be used to have player react certain ways in cutscenes based on our interactions and actions. That way, even if the player is in a story that doesn't put them on that high of an importance level, we'd still be contributing to the story in our own way and how characters act.
-The start. I disliked how they said "this is for the grand trial!". It didn't feel like th other games to me, in which it was for the professor and for your own, self-guided journey. It already started feeling scripted out here.
-Lillie. Lillie imo was a terrible character and they spent way too much time focusing on her. Gladion, Hau and the sort were, as a result, underdeveloped. The only other really developed character was Lusamine, whom I'm about to complain about as well.
-Lusamine is overrated and not really that dark. I get the whole relationship with Lillie thing, but it's really not enough to keep a plotline going. It feels like it gets repetitive and stereotypical, and doesn't take quite the risks as other plotlines do. Compare this to BW2's where Ghetsis literally threatens to freeze the player (which to me is pretty much threatening to kill), or when Cyrus betrays an entire team and goes ahead with his plans.
-As I said earlier, other characters were underdeveloped. Gladion in particular stood out to me as someone who could have been elaborated on a lot more. He had an interesting premise as a rebel against his mom who would actually fight back to stop her (unlike Lillie who was pretty much a damsel-in-distress under a not-so-clever disguise), yet was shoved aside in favor of Lillie, Lillie and more Lillie. Hau too could have been made to be more - ala Hugh in BW2, or Silver in HGSS (with the Celebi event).
-I know I'm sounding redundant, but the Trail Captains and Kahunas sucked. In earlier gens, we'd always have like one badass gym leader or Champion who would take charge of defeating the villainous team - like how Lance did in HGSS, and Steven Stone, and Cynthia - but not here. None really seemed exciting. And Professor Kukui imo is a shoddy replacement because he didn't really do much vs at least Team Skull.
-The Aether Foundation was undeveloped. I mean, Team Skull had plenty of personality and imo are one of the best teams we've had thus far, but the Aether Foundation did jack. They pretty much said "We're here to help Pokemon and give them new homes :)!" but when they were truly discovered for what they were, they pretty much said "Oh no! We've been caught! Time to pathetically fight back!". That's about it for the Foundation.
Before we start I just want to say you're not wrong in your opinions, they're your opinions afterall. I just wanted to give my perspective on some of things you mentioned:
Island Challenge: I think the issue here isn't the Island Challenge itself but the game hand holding you through it. Professor Kukui constantly popping up as well as Hau and Lillie following not that far behind didn't make it feel you were doing that much on your own. True, in BW and XY you were also with a group of friends for most of your journey, but in those games it felt like they had them doing other things letting you go on and do your own thing until you bump into them or they purposely waited to meet back up with you. But SM? A lot of the time it felt like they were either right behind or slightly ahead of you, keeping pace with you so they can initiate a trivial cutscene.
Lillie... And Others: I'm curious whether it's not Lillie herself that's the problem but the over focus on her. Personally I liked Lillie's story arc on the whole, but I can agree maybe they could have eased off on it, especially during the beginning. Gladion I actually felt had a nice amount of screen time though I wouldn't complain if they gave him more. Like have a scene of him interacting with Plumeria and/or Guzma, him actually disciplining some Skull grunts, or had him in Po Town (we never learned how he heard about Lillie's kidnapping so fast). Finally, despite Hau being with you most of the way he barely develops. I think not only may he needed some more development early on but also maybe traveled with you and Lillie to the final island. Just seems strange he would run off after all that to train. Actually, I think maybe both needed to have a side quest after the Aether Paradise raid. With Gladion you can help him re-establish order within Aether Paradise by fishing out members who are either Team Skull in disguise or are loyal to Faba who's trying to seize power. For Hau, if he's not going with you to the final island I'd say maybe have him going around the islands to check if things are alright after the Ultra Beasts were unleashed (and maybe give us a glimpse of some of the Ultra Beasts while helping out with damages they caused).
Lusamine: No, Lusamine is dark, but a personal level of dark. Cyrus, Ghetsis, and Lysandre were a more grander scale of dark, as in their goal was to take over the world. While Lusamine's actions did put the world in peril, that's not what's dark about her. She lacks empathy and shows what a human with no inhibitions would be like. She was perfectly ready to kill both the player and Lillie in the Ultra Space all because Lillie told her off. As or cliche, I don't see how. If anything, the other villains were cliche as they just wanted to take over the world like a cartoon villain.
Captains & Kahunas: I think this is a situation where, since it was attempted to give all characters some personality, it results in none standing out. In past games we had Gym Leaders where the only thing they did was be a boss, though usually having one or two which actually did something. In SM they tried giving all the Captains & Kahuna something to do outside their role of being a boss but any that had a bigger role was lost in the shuffle. Had this not been done I'd think Acerola and Nanu would be the standouts as they had story roles.
Aether Foundation: Yeah, the Aether Foundation needed more screen time before the twist happened. They were established... and that's it. We needed more interaction with them, especially the higher ranking members, before they did the twist they were the real bad guys. Once again, doing side quests for them wouldn't have been a bad idea, and with them having members and building all over you can have them give out different quests pertaining to the area to make it feel like they have an encompassing presence throughout Alola.