Hmm, perhaps this is a wayward topic, given how anthropomorphism (non-human characters having humanlike traits) for Pokemon typically translates as things akin to Pokemon Mystery Dungeon.
I came across the subject of anthropomorphic Pokemon in fanfiction a few years, and I've been trying to include them in some offbranching fanfics I've been writing in that time. At first, I limited them to a PMD story featuring several Fakemon that were already humanlike by default. However, I've been finding myself using such characters more and more frequently, even in fiction that's not strictly about them. One things I've been wondering is how do people feel about having such characters in fanfics. Do they seem to make the plot less believable, or perhaps just less serious than the concept is really supposed to be? I've kind of acquired a liking for them myself, but that's probably just because I'm used to including them in my stories.
I know this is a pretty general answer, but it's all about how they're portrayed. I'm all for it, if it makes sense. There's currently a fic on here that basically replaces humans with various pokemon and has a whole medieval feel and how a society like that might have worked and it's working great. One of my favorites, in fact.
The tricky part, however, is the reasoning behind it. What strengths and weaknesses do each pokemon posses that will help or hinder it in the story? If the writer can pull it off, I will like it. If the writer, however, is just replacing humans for the sake of calling it a fanfic and doesn't so anything special with it, then we have a problem.
It mostly depends on how far are you willing to stretch "human-like traits", in my opinion.
I mean, a Pokémon like Cubone or Grovyle can have prehensile ability close to a human's (and in Grovyle's case, argaubly better). Stretching oppossable thumbs capability to Pokémon like Golduck or Aggron is harder to do, but can be done sensibly. But Lanturn? Fearow? If you go that way then you go into Donald Duck territory, where they can easily grab any object with their "finger wings".
Also do note that antropomorphism means morphism - shape, and anthrophos - human. Yet you are writing a Pokémon fanfic focused on Pokémon. So a big question is what do humans have that Pokémon don't AND you would have to give them for the story to work?
Is it culture or society? The manga, anime and PMD go to diverse lengths to show that Pokémon species do have cultures - just Pokémonal and not human ones, so don't mistake being able to build skyscapers for being able to build "cities" (there are diverse examples in our real world, such as bees and ants). Movie 4 at least suggests wild Pokémon have some sort of communal law, not to mention the indications given by Sinnoh lore.
Is it "advanced reasoning"? The various canons portray Pokémon in diverse levels of sapience and self-awareness, but all of them agree, and at least the anime showcases more explicitly, that Pokémon have much more advanced "feeling" that humans have, and have a wider array of communications as well (the Digglett and dam episode being a prime example). Even without the exaggerated Pokédex entries, it can be agreeded that at least Pokémon like Metagross or Alakazam can acquire lots of knowledge, and in general it can be assumed that many Pokémon such as Rotom or Voltorb should be able to interact at full capacity with advanced human technology (I borrowed headcanon from a friend, in fact, that says with Pokémon like Rotom or Porygon around you can mount your own ISP, and they can serve as living GPS as well).
Or are you thinking "but we can build spaceships and level mountains to create crops/cities"? Then Clefairy and Tyranitar, in the very least would like to have a word with you. They just don't follow the purposes and paperwork humans do.
Then there's also the problematic trend of anthropomorphising certain species of Pokémon in... certain ways, but we'd better not go there.
In general, I can say Pokémon should be written about as if they were Pokémon, that is creatures of their own species and with their own biology and the traits that come with it, and not just humans with superpowers - for that one can just go read or write Justice League, Marvel's X-Men or any assortment of competitors in that industry.