I recently watched a review comparing all of the versions of Ocarina of Time, and in it the reviewer said something which I think is very relevant to adventure games.
He said, and I quote "The purpose of story in gaming is to contextualize gameplay, so it doesn't come off as a laundry list of arbitrary tasks."
And I've come across several reviews and complaints about adventure games (even on this forum), where they have said that the game is about giving a bit of story, and then blocking you with a puzzle, which you then solve, and then get a bit more story before being blocked again, making the two exclusive to each other.
But that quote pretty much sums up my thoughts, which is that story and gameplay should NOT be mutually exclusive in an adventure game (or any game for that matter), but should instead work together. And the problem is, most people who make adventure games don't realize that, and as such they make them exclusive to each other. This isn't a problem with the genre itself, but rather with the attitudes of the creators.
I'd love to discuss this a bit more in-depth, and get other people's thoughts on the matter.
I agree that this is a problem in bad adventure games, one infamous example is the cookie baking puzzle from
Still Life, which is a game about a policewoman investigating a series of brutal murders inspired by Jack the Ripper. The game contains gruesome imagery and violence, yet at one point the plot grinds to a screeching halt because the protagonist's dad asks her to bake some gingerbread men, and what then follows is a long puzzle trying to decipher the encrypted recipe in her grandmothers cookbook. Even if you look aside the fact that no sane person would encrypt the recipe for freaking gingerbread, the plot so far has been about the hunt for a serial killer, and by having the protagonist stop to make cookies just removes a great deal of the sense of urgency and danger.
Gameplay should vary depending on the character you play as, and playing a crime detective on a case shouldn't be the same and contain the same puzzles as a baker or jobless slacker, and that means that the puzzles should be different as well.
I think that indie games did bring some new elements to adventure games, namely a bleaker environment, more serious themes, and some new puzzles at times, but it is true that we also see huge repetition of some specific story lines. To name one which exists in a very large number of indie adventures: amnesiac character, character who did some crime and then is unaware, and/or multiple personality.
I definitely think there are some very overused tropes in adventure games, such as the amnesiac character you mentioned. It's almost always a white man with short dark hair in his 30s who's wearing generic standard clothes (often jeans and T-shirt without logo, occasionally a leather jacket)and 9 times out of 10 the "big plot twist" is that he either was the killer all along, or that he was framed for a murder and the real killer made him forget what happened.
But there is a second character archetype I'm also getting a tad tired of seeing in adventure games, let's call it the Unlovable Rogue, for when the developers clearly tried to make the protagonist come across as a lovable rouge in the vein of Indiana Jones or Inigo Montoya but ended up making them a smug jerk instead. If the character is male, he'll be a messy slacker with a gross and untidy home and work space and of course he's lost vital items and equipment in there and forces the player to dig through it all, plus he has a tendency to tell mean spirited and bigoted jokes at other characters expense that aren't jokes as much as they're just random mean comments bordering on bullying. If the character is female, they usually face and body of a Barbie doll but compensate for it by being rude and sassy in a lame attempt to be a "strong female character". All of these characters also often have a tendency to have a detached "Why should I care" attitude towards things, but if the player character can't be arsed to care about the plot, why should the player?
Compare that to April Ryan, who starts off as kind of a snarky slacker, but as soon as she realizes strange things are afoot she does take the whole thing seriously and towards the end of the game she's overcome most of her personal flaws.
Or Look at Guybrush Threepwood, while he comes across as messy and silly, he does have a friendly attitude and feel some actual enthusiasm for what he's doing.
And there's also the stupid idea that nonsensical puzzles are perfectly fine if the protagonist crack a joke about how nonsensical the puzzle is,
but in reality it's just the game design equivalent of somebody putting their foot in their mouth and immedatly going "lol, just kidding!" afterwards.