I remember ranting about how bad of a choice keeping the player a faceless mute (who should be played by Orlando Bloom) was when I got to a similar point in Pokemon S/M. I actually like Lillie and it would have been a neat idea if they made her the main. Heck, she even has a connection with the game's mascot. Pity the internet seems to have made her a living meme and ruined the word "bag" as a result.
Piggybacking off this, this is the first time I feel in a Pokemon game where the protagonist actually felt like a detriment to the game. No matter what the scene is, the character always has that empty "=)" on his/her face and it's jarring at times. There's moments where Lillie is pouring herself emotionally, and your character just stands there smiling like "wait, why are we happy about this?" Now a silent Pokemon protagonist is a given, but they could at least bother to let the character show some emotion, if at least just showing facial expressions to match the scene.
I know lolPokemon plot!!!, but the only reason other games got away with it is because their plot was so minor (Black/White 1 aside, and being a sprite based game, obviously expectations in presentation are different) but Sun/Moon actually makes an attempt at a serious jRPG style plot, with actual characters, so when we have Lillie, Hau or Gladion all showing varying expressions, development, personality, etc., and then you just have the character going "=)" regardless, it's painful. A parallel this would be Suikoden 5 where you have all these colorful, well written characters...talking to someone who can't respond if there isn't a text prompt, and it stands out a lot.
It also stands out when playing games like FF14 or XBCX alongside Sun/Moon which also have Avatar protagonists (well...XBCX, you're not really the protagonist, just the PoV character), but they let your character at least show visual reactions. Nothing major, just stuff like a surprise face, a head shake, etc.
Actually I give props to FF14 for this further since while it doesn't avoid the "Silent Protagonist Avatar IS PERFECT!!!" syndrome, it at least does it with a sense of self awareness, having occasional nods to the fact that the writers realize they wrote you that way and are just going with it. Heck, in 3.5, Thancred has a line that is essentially "I mean, we could put the Warrior of Light as the leader...but s/he's too busy being ABSOLUTELY PERFECT AT EVERYTHING S/HE DOES that they won't have time to be leader." Or even earlier, Cid says something like "So...we need someone to save the world? Well how about it, Warrior of Light? You're basically an expert at this!" Hey, if you can't actually make a silent protagonist flawed, you can at least acknowledge that you know you accidentally made them perfect and play to that.