Capitalizing Pokemon or not?

Pokemon and the names of species generally are printed with the first letter capitalized in game text. My autocorrect likes to capitalize it as well. However, there are definitely some people out there who hate seeing the noun capitalized. I'm really not sure what to do because I see people doing both. How do you do it?

if the trainer is calling their Pokemon by the species name, I'd captitalise it because it is a proper name. For narration purposes, I do lowercase it if I am saying it as a noun.

ex: a pikachu was running through the woods
ex2: "Magneton, use thundershock!"

I always capitalize the majority of Pokemon terms that are clearly from the canon. (It's things like "gym leaders" and "badges" that I tend to waffle on.) The reason why I capitalize them is because I stick to the "it's a copyrighted term that's capitalized in canon, I'm going to capitalize it myself."

The answer to how you should do it is: it doesn't matter what you capitalize or how. I've seen writers follow the same rules that I do (capitalize everything) or do it the same way Huikyeong does (when it's a proper noun but the species name is lower-case). You can go any which way. The only sure answer is to be consistent with how you do it.

I capitalized Pokemon names same reason as Astinus does, but I toyed with the idea of not capitalizing them often since I know many writers are doing the same. But yeah, me personally I'm not picky if someone capitalizes the Pokemon's name or not as long as they're consistent.

You will run into some folks who say that capitalizing pokemon nouns when you're not strictly using them as proper nouns is a crime against the English language, but I think it's safe to ignore them. The reality is that this is fanfiction for a franchise that uses idiosyncratic capitalization in all of its official media. You're not obliged to "correct" the style of the source material, no more than you would be to correct Homestuck's spelling, grammar, and capitalization in a spin-off story.

That said, you're not obliged to adhere to every facet of the source material either, and that includes leeway to change its code of style to more resemble regular literature. As Bay and Astinus have said, the most important thing is to be consistent. You can decide to make an exception of just about any rule as long as you fully understand the rule itself and why you're making an exception.

Personally, I pick a capitalization scheme on a fic-by-fic basis. Sometimes I want it to sound like a more direct video-game adaptation, other times I want something that's more grounded. Sometimes I'm working with a universe where people refer to a pokemon collectively as a species in the singular. (Not "charmander are short and wolves are strong," or "Charmander are short and wolves are strong," but "Charmander is short and Wolf is strong.") This I think is both similar to how Pokedex entries are written and makes sense for spiritual cultures.

One more thought, here's why I think the official media capitalizes words all over the place: if you don't know what you're reading, "seel," "onix," "dewgong," etc. are confusing and just make it look like the writer can't spell. The capitalization is easy shorthand to convey that these are invented, Pokemon-specific terms and not the Queen's English. I've also found that even though I'm pretty knowledgeable about Pokemon, the capitalization helps in fics I'm reading helps when there's a 4th or 7th gen pokemon that I don't recognize. It becomes, "Oh, that's a Pokemon," instead of, "What's this gibberish?"

tl;dr: Keep Calm and Be Consistent

I tend to just capitalize them all the time, really unaware people actually get offended by such things xD

I think as long as you stay consistent and not fluctuate too much between capitalizing and uncapitalizing you should be fine.