Alignment - Hell with alignment. I'm not really into the Great Cosmic Forces clashing right now - it can work awesomely, as it does in the background of the current Hill Cantons campaign, but it's not my bag in terms of what I want as a setting element. And if you're not going to have Zelaznyesque or Moorcockian grand sweeping alignments, then you don't particularly want it as a behavioral guide for PCs. Or at least I don't.
|Sure, it never seems to bother Nodwick any...|
Experience - I know I want to add XP for exploration and discovery, beyond monsters slain and treasure looted, but I need to hack together (or steal) an effective system for doling that out. Or just award arbitrary amounts, but that seems a bit off. This might be something to loot from D&D 5e if they put together something cool; I know that there's been some discussion of a more gamey exploration element.
Movement Rates - Rey mentioned that he lists things on a Very Slow - Very Fast axis. Hell, I don't even bother listing them.
Rey lists Flat Bonus Magic Weapons/Armor, but I don't think that even counts, because everygoddamnone has realized by this point that there isn't anything interesting in a +1 weapon without giving it context and personality.
Magic, In General - building off of the last bullet point, I've cut direct-damage spells and resurrection magic from Legacy of the Bieth. (As I say this I realize that I might want to have a resurrection mechanic, but it's far more involved than finding a sufficiently high-level priest, and of the Unfortunate Consequences variety.)
Weaponry - Any class can use any weapon; this primarily shows up in restricting cleric weapon selection, and honestly it doesn't matter that much if your cleric is using a mace or spear or shamshir they're going to get mutated and die horribly just like everyone else.
The Mark of Amber review has stalled out because work and studies have ramped up a bit, but it is not forgotten. (Nor are, y'know, actual game materials for this setting.)