Removal of gyms (even if Gen 6 made them way too easy), overrated evil team (Team Skull just seems uninspired and without a purpose to me), lack of replay value, lackluster online features, etc.
Island Challenge Instead Of Gyms: While I don't mind going away from the Gym system once in a while, I don't think Gen VII's Island Challenge was a proper replacement. The idea is sound, instead of battling through a Gym you complete a Trial task, defeat the Totem Pokemon, and once you completed all Trials you have a Grand Trial which is a battle against island Kahuna; repeat once per island. However the problem was with the Trials, they felt off.
First, each island had it's own amount of Trials (Melemele has one, Akala has three, Ula'ula has two, and Poni has one/two). I get they want to make each island feel unique though Melemele only having one makes it feel kind of short (even though you still have to explore the rest of the island anyway). I felt Melemele should at least had one more, I'm alright with Poni only having one (officially) due to it being scarcely populated but Melemele is a major island.
Second, the Trials themselves are hit and miss. Now I'm not talking about the Totem battles, those are fine and actually require strategy. The "puzzle" portion of the Trials sometimes felt they didn't have much thought put into them. Ones I thought were fine were Ilima, Mallow, & Acerola as they involved exploring the area which was something different. But Lana's & Dragon Trial was pretty straight forward, Kiawe's was a joke, and Sophocles' was just a gauntlet battle. Also, all the battles were against easy to beat wild Pokemon, except the one time you battled the Hiker in Kiawe's challenge. And while the Hiker was easy to beat also, there's just something about facing a Trainer which feels more satisfying then a plain wild Pokemon. Also, the Trials are supposed to be different from Gyms but if I'm doing a puzzle and having battles while doing it, what is the difference aside the aesthetic?
Third, the Captains sometimes felt pointless. It's implied the Captains take care of the Trial area, but the only ones that felt "necessary" for their Trial was Mallow and Sophocles. All the others had a passive role in which case why are you here? If I were to redo the Trails a bit I would get rid of all the incidental battles during the Trial and instead had you needing to defeat the Captain to prove you can do the Trial and take on the Totem Pokemon. That would have been different, a beginning and ending boss with an uninterrupted puzzle segment between them.
Also, it all ends with the Pokemon League, Elite Four, and Champion battle anyway. If you're going to toss out the Gyms then toss out the Pokemon League entirely. The Island Challenge feels like they did something different for the sake of doing something different instead of having a fully thought out new challenge system.
Eitherway, I'm ready for Gyms again and collecting Badges again (which is another small nitpick. Yes, Badges do nothing, Z-Crystals actually help you in battle, and upon completing a Grand Trial we did get a Stamp. But I just like to see the Badge designs and how they reflect the Gym Leader we fought, curious what the "Badge" for the Captains would have looked like (and maybe for the Kahuna though they give out the Stamps)).
Overrated Team: The thing about Team Skull is that they had their spotlight taken from them. I'm a bit bias as I like Team Skull and really got into seeing the "true side" of them upon getting to Po Town, the tonal shift was surprising and exciting. Sadly, that is where any resemblance of Team Skull being a threat stops as the Aether Foundation plot takes complete control. Now it felt like a smooth transition and made sense (at least in vanilla SM), but the final villains of the plot weren't the thugs you been battling along the way but rather suddenly the animal & environmental help group because their leader is currently insane. And after all that Team Skull disbands.
Lack Of Replay: That's a complain I think for all Pokemon games, you're not really mean to replay the story once your done with it. Not that this isn't a problem, GF had lately been bad with post game content and would it really be that difficult to add a difficulty setting and an additional save file that let's us replay the game without losing all we did and our Pokemon in the "main" save file? One of the many places GF is archaic is with the save system, saved data cannot be that much they can't put in a few more save slots or have special save slots become available to provide a way to play the game again or provide a different experience.