Reviver Seeds
I like to think of them as something like smelling salts. Something to help someone regain consciousness, not something that brings back the dead. Having an item that brings the dead back is a quick road to Dragonball Z territory, where story deaths feel cheap because they aren't permanent.

Carnivorous Pokemon
Pokedex says some pokemon eat meat. In fact it specifically says some pokemon eat other pokemon. Any more advanced society would frown upon murder so I would go with carnivorous pokemon naturally eat meat but now eat a substitute instead.

Badge Teleportation
I don't like badge teleportation for the same reason I don't like reviver seeds bringing back the dead. Makes bad situations seem lesser when you can teleport out of them. I've always liked the badges to be more of a system to make a call for help.

Moves
I never use move names in my own story. I will describe them as using a specific move but avoid giving them the standard names as that feels to trainer related to me. This is from the first chapter of my story, "Pulling all the power he had he opened his mouth wide and focused it. He was rewarded by a look of surprise on the Zangoose's face just before a ball of pure dark aura exploded from his maw, knocking the Zangoose clear from his victim." That is usually how I handle pokemon moves.
As far as limits go, I think they should know more as they gain experience and age. Having a number limit to the moves is a game mechanic that I don't like bringing into stories.

Fire Types
It's water guys, all living things are made of it. Makes no sense for water to wipe out a fire type just with contact. If that was true then a simple rain storm would be catastrophic event in some areas. It would be at odds with their natural ability and would therefor be unpleasant and probably weaken them, but shouldn't do any physical harm.