Preface: I'm not saying referential humour (making references to other things) is bad and I'm not saying metahumour ("breaking the fourth wall" in a loose sense) is bad. This is just my thoughts on the subject given recent exposure to it, my thoughts on why the problems inherent with them do exist, and how budding writers can nip this issue in the bud before it starts to fester in their own works.
I play a lot of fangames. Probably more than I should, but I do love each experience. It's the kind of series where every developer has their own take on how to balance things, and each player can come up with their own preferred ways to enjoy the playing field that's been set out for them. I also have a lot of experience playing other games, and I'm an avid reader, so I'd like to believe that the opinions I'll be expressing here are based on a diverse set of experiences among a number of broad categories.
Something that I've noticed a lot in Pokemon fangames, as well as most modern amateurish works (amateur here meaning unprofessional in a strict sense of the word, not to be used as an insult by any means), is that there's an overuse and sometimes even a reliance on references to other media within the writing. This is done for a variety of reasons -- too many to list here, but I'll still make an attempt at listing the main ones that I've personally noticed.
1. Canned laughter, as I'll refer to it. This is when a creator is basically copying and pasting something from another piece of media into their own, done as a reference but often with little to no context and even more often with no relevance to the story, setting, or events at hand. This is when you'll talk to NPCs and they'll make reference to something just for the sake of making a reference to it, as a joke.
2. Filler. This is when a creator's basically overstepped their own abilities, and they start relying on references to fill the gaps in their own writing. You'll notice this, for example, among a lot of NPC trainer dialogue. When a creator fills a route or a dungeon with fodder trainers but runs out of things for them to say halfway in, leaving the other half of the trainers being awkward references to other things.
From this point on I'll be referring to referential humour and metahumour together as just "referential humour" to save on time.
Again, there's nothing wrong with referential humour, nor am I implying that it needs to be cut out or even reduced. What I want writers to take away from this topic is how they're applying it practically to their own stories. Most if not all the writing in a game or a story should serve to further the game or story's purpose. That's where a lot of referential humour fails; it's a hard-stop that serves not to further its own story, but the pull the reader out and have them focus on a different story entirely. There was a game I played recently that would constantly make Spongebob references. Both me and my audience eventually started to just mock the writing of the game, because it would be trying to make us take its story seriously while interrupting us every two or three text boxes to either reference Spongebob or make any number of "this game mechanic wouldn't make sense in real life" jokes.
References in games can be done well, but they have to be done sparingly and appropriately. Restraint is the key to any good piece of writing. Knowing how to maintain a consistent mood when necessary throughout a scene is difficult, but manageable by even the most novice of writers. The key is to have confidence in one's own work, and to avoid falling into traps of trying to "fill in the blanks" with canned references that ultimately just throw off the pacing of the story and destroy the immersion for anyone trying to get invested in them. The best kinds of references are subtle enough that people who don't get the reference will think that it's just another piece of the world dressing without having to stop and question if the writing is trying to make a joke that they didn't get, or if it's just an awkward stumble on the part of the writer.
I wanted to make this thread because I know there are developers that spend hours making their games, and might eventually become out of touch with the people that will eventually be playing the game they've been making. To those developers and to those writers in similar situations, I'll leave on this note:
References on their own aren't charming or funny. You need to be able to have the proper set-up in place for them, or they'll fall flat on their face. If you're ever at a loss on what to write, or what to make a generic trainer say, don't turn to references as your default method of solving that problem. Take a break to think of something on your own, or just delete the trainer or NPC entirely. Almost no one likes fodder trainers, and if you were to combine two trainers with two mons each into a single trainer with four mons, I can almost guarantee you that people would find it more engaging.
The writing in any story serves specifically to further the story. If you're making references that serve no purpose, then you're doing nothing but undermining your own writing, and potentially destroying the entire experience for the people that would otherwise be the most invested in it.