Loyalties, or Alignment by Another Name
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So, I am not a big fan of the loyalties system, but not everything in here is a wash. First, though not most importantly, I am loving the picture of Seelah standing at a signpost with directions (in opposite directions, of course) to the burning orphanage and the anti-paladin's castle. It's hilarious. Seelah also looks pretty badass. The Creatures, Spells, and Effects section has some great suggestions for how you could make some changes to the game. Let's discuss:
This is really just mechanical advice. If you take alignment completely out of your game, there are a few adjustments you'll need to make so that the rest of the power system functions. For instance, monsters with alignment-related spells or spell-like abilities will need new ones of similar power. Abilities that only target some types of alignment will need to be replaced. This is pretty obvious, but it's good that the designers considered this. I'd have preferred that they consider this option for removing alignment first, but this is a start.
Basically, you adopt the loyalties system and let spells, abilities, etc. that affect alignments affect those who have loyalties to law, chaos, good, evil, etc. The only way that this could really be made fun would be to let those four all conflict with balance. But, I'm betting you wouldn't see anyone with loyalties to neutrality after that...This seems meh.
Actually, I quite like this both as a player and as a GM. Let the creatures of the outer planes continue playing a role of ultimate good or evil but recognize that humans are cut from more complex cloth. Detect evil might or might not pick up the evil-acting warlord, but it will find the devil hiding in the tower. The challenges here would be how to deal with clerics, paladins, and antipaladins. Not a huge headache, but certainly not the most fun.
Radiant and Shadow
Rather than having the spells deal alignment-based damage, just reconfigure them as something else. Law, chaos, good, and evil all become different types of energy. Further, creatures with an affinity for these energies are likely immune to them. BUT, and this is the kicker, the energies aren't tied to specific moral codes. This could make for an interesting one-shot game, but I'm just not finding it inspiring for something long term.
I think that this is my favorite of the options--not surprisingly, it's got the longest set of text about it. Basically, you get rid of all all alignment-based effects except good ones. Then, those effects are actualized by working on those who are opposite of their user. For instance, detect evil doesn't discover people who are evil. Rather, it discovers people who hold views opposed to your own. It's unclear if opposed to your own means opposing viewpoints or animus. The book suggests fixing this with the loyalty system. I think GM fiat works best. Same goes for whether or not holy swords work on someone. Fun thing about this concept: it means that spells like detect evil and the extra effects of holy weapons will sometimes work on enemies and won't at other times--including for the same enemy. That's a fun storytelling tool to hold in your pocket as a GM.