Creative liberties? Where do I start?
Okay, for a start, I guess I could mention that my story is set in my own universe. And there are no humans. That's quite a notable one.
This originated, weirdly, from conkeldurr's pokedex entry. It said that conkeldurr taught humans how to make concrete originally, which made me wonder if pokemon even need humans for a sophisticated world. I put on my proverbial philosophical hat and answered 'no'. In fact, I believe the world would be very similar.
What do humans actually provide that pokemon can't do? There are pokemon with hands who could write, and make things. Fighting types are much stronger than us, and would make better builders. There are pokemon cleverer than we are (although generally for the purposes of the story, intelligence is generalised, so more intelligent pokemon are brought down and less intelligent ones are raised up, to an extent at least; I felt it was necessary for a sophisticated society). So that results in a society not too different to a human one.
The setting I settled on for the actual story is more of a fantasy-esque thing, which is also a notable creative liberty. I thought this would fit better with things like pokemon moves, which are not unlike the sort of magic you'd find in a normal fantasy story. The actual 'moves' used in the story, by the way, are more like 'references' of sorts to the ingame moves, rather than being the exact same thing (and there are a lot of other actions which don't fit moves at all). This opens up possibilities for pokemon learning moves which they couldn't normally learn, for example, one of my characters is a vaporeon who works as a ritualist, which gives him access to lots of ghost-esque powers, for example, he uses a spell similar to shadow ball a lot, almost as his personal signature. A lot of moves like this are based more on someone's training and skills than their species.
This brings me onto another point, which is that ghosts are not treated as 'regular' pokemon like in the games and stuff. They're more like incorporeal, other-worldly spirits, something not uncommon in fantasy. Accomplished magicians (often, but not necessarily psychic or dark types) can train to summon ghosts into the material world from the 'void' (if you have a better/more original name, please tell me) where they normally dwell, and make the spirits perform tasks for them. Maelstrom, the aforementioned vaporeon, is quite good at this.
Other than ghosts, types are largely not paid much attention to. Instead, I focus on what something's body is actually like. A victreebel would still be weak to fire because its a plant, but leafeon which is a fox would be able to take fire much more effectively (if still not well) because only part of its body is plantlike. Similarly, there's no reason why an espeon could resist being punched substantially better than an umbreon, since they have very similar body structures and all.
Hmmm, well that's quite a lot of creative liberties, but it's by no means a complete list. If I really started thinking about this, it may only be the tip of the iceberg. Oh, and if anyone has questions or issues with what might not work, and stuff, it might be handy for you to bring that up. So, yeah, I'd probably appreciate it. Anyway, this post is long enough, so I may just stop rambling now.