I've been GMing and playing in tabletop RPGs for about 25 years now (since AD&D 2nd Ed.)
I agree that this "players vs GM" confuses the hell out of me. If a GM wants to kill his players, it's super easy. Nothing in the rules says the GM cannot force the players into 3 back-to-back extreme challenge encounters. 4th edition D&D "guaranteed" the players a 5 minute rest between encounters (to recover encounter powers), but that's about the safest the rules have ever made players from a cruel GM.
GMs have ALWAYS had far far too much power. That's their job. If a player can show up to a table and boss the GM around, they're likely going to make the game less fun for the other players.
And if not - if the GM is making the game less fun for all the players, and RulesExpertJohn is challenging him and trying to fix it, the better solution is usually just to find a different GM, not get into gritty rules lawyering.
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The Rulebooks are tools and guidelines to help a GM make a meaningful and structured experience for the players. And they are there so that the players are on equal footing with each other (not with the GM).
In fact, page 8 of Core Rulebook (2.0):
"The GM is in charge of the story and world."
"...being a GM is a challenge, requiring you to adjudicate the rules..."
"the only thing that matters is that everyone has a good time, and that includes you"
And on page 483 (ch10: Game Mastering):
"As Game Master, you have the final say on how the world AND RULES function, and how nonplayer characters act. This rule's purpose is to make the game run smoothly, with one guiding hand ensuring consistency. It's not intended to make one player dictator over the rest of the group."
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These quotes point out quite clearly that a GM saying "no, you can't" is perfectly ok. The GM is in charge of the rules.
Pathfinder Society play bends this in favor of the players some, but in the end, it is still the GM in charge - and fully capable of killing an entire party off if he/she decides to.
Hell, the DM makes tons of dice rolls behind the screen - which is yet another method they can 'cheat' (for good or for ill). If the GM has a free license to cheat, what would you (as a player) hope to accomplish by backing the GM into a rules corner, and/or making him hate you as a player?
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The GM has all the power. But he also is the one most responsible for making the game fun. And if players don't like a GM, the power *they* have is to not play.
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With regards to rarity, I love the simplicity of the system.
Common = in the game for everyone
Uncommon = in the game for players whose background/character is appropriate, or for the GM to allow for other characters
Rare = GM's choice when/where to allow it
If you're a player, and want uncommon gear(s), it should fit into your characters ancestry/background. If your build/idea won't work without rare gear, I think you should be asking yourself why play such a high maintenance idea in a game with a GM you aren't familiar with.