There are some very stupid weaknesses like Bug weakening Psychic and Dark? I get that Bug may defensively resist those types but why have bug do better damage to them offensively? Dumb!
And why does Rock weaken Fire? I get Ground but Rock?
There are definately type match ups that don't really make sense, but again that is for our world. Maybe Bug's in the Pokemon world have a natural anti-Psychic/Dark field. Perhaps Rock type moves have anti-oxidizing effect that removes a small amount of oxygen from wherever they strike. I don't know how EXACTLY how things work in the Pokemon world, but I accept that they do.
If you brought in the original creators of Pokemon and asked them, 'how the hell does a bug beat a psychic?' they might not even give you a good answer. But these are the rules that they have set for us, so we will also abide by them.
Maybe you should start a thread about the problems you have with Pokemon. Or a thread about what changes to Pokemon you would make. Or maybe a thread about a brand new world that has similarities with Pokemon but is more logical in our sense (be careful, you will likely have a super type that beats all other types).
No point complaining in this thread about how your choices need caveats in order for you to want them lol. Fire Gym will still be a very powerful gym, regardless of how many weaknesses they have. Or sh*t, start a thread identical to this one but instead of us going there, Pokemon coming to our world, that would certainly change things.
Otherwise, in the immortal words of Justin Timberlake 'Cry me a river.'