Obviously, except for like Joltik and Dratini, none of them are going into your pocket... if pockets are even a thing. It always bothered me that the PMD series called them "Pokémon" anyway, even though I realize that's just because nobody but like four people would have any idea what was going on if you heard about "creatures" or "monsters" throughout the plot without the thing in the title showing up anywhere... but fanfic doesn't have that limitation. Just go by species name? Call them creatures?
There are a number of options for when you want to refer to Pokémon in an abstract or collective sense and none of them is bad, really.
* You can just call them Pokémon as if they would in-universe call themselves that. Maybe in their universe the term means something different that they happen to fit (like let's say a foreign term from the Poké-Náhuatl equivalent of "Po-kim-han").
* You can call them Pokémon because something else calls them that. Doesn't matter what: GtI and PSMD make it clear that there are things out there in the PMD verses that are not Pokémon, so maybe something (an ancient human? dun dun duuuuuuun) called them that.
* You can just call them Pokémon and invoke "Translation Microbes" and leave it at that. It's not a situation exclusive to PMD 'verses, even, so likely no one will bat an eye (so far in fandom, no one has made strong fuss about it).
* The movieverse uses at some point the term "majū" or "magical creatures" for them. Maybe adapt something like that. It does have some charm, but you'll probs have to spend a bit of time every 25 chapters or so reminding the audience somehow that yes, these are Pokémon and not something else.