I think the main pain in the "alignment matters" occurs when you want to use the ruleset in a world with an alternative alignment system, no alignment system, or a world where typically alignment runs second compared to practicality and survival in a harsh situation. (I just posted something noting that in the campaign I play in currently, I have an exalted monk (with toned-down Vow of Poverty), and we're generally working to help support Irongate against the Scarlet Brotherhood, but head of the Irongate secret service is almost certainly lawful evil.)
Anyway, I think some people have (for some reason) lost sight of the fact that if you rule 0 away alignment, you can change things around a lot. I'm fond of the d20 Modern allegiance system (you can have up to three listed allegiances, in order of importance. Those allegiances might include Good, Evil, Law, or Chaos, but more likely include something like: CIA, United States, Secret Order of Holy Onion Bagel. Meaning that allegiance to the CIA comes before allegiance to the US itself, comes before allegiance to the SOoHOB.) I like it mainly because in a situation like the Irongate campaign, it makes it more clear what's going on: the evil SS guy's allegiance is really to Irongate, and *maybe* to Law after that. All he cares about is making Irongate safe, and if he has to torture people, so be it. My character's allegiance, on the other hand, is more like: Good, Zuoken, Irongate. She cares about Good above all else, the precepts of Zuoken's followers second, and Irongate only after both of those.
Of course, the allegiance system can be made to fit with the standard alignment system: first, you say that only people who *very strongly* believe in an alignment have an alignment as an allegiance. A traditional lawful good fighter probably wouldn't have Law or Good on his allegiances. A paladin might have one or both, or simply have a LG deity. I'd say that it's appropriate to say that you can choose any of the traditional alignments to have an allegiance to (so you don't need to use two allegiance slots on Law and Good... although doing so allows you to distinguish which comes first in your character's mind.)
On another axis: I've been thinking about how I'd use MoI in a setting that has no alignment whatsoever, and came up with the idea that the different "alignments" could be treated as different schools of incarnum use. Now instead of having to be good, lawful, chaotic, or evil to be an incarnate, and that focus determining whether you focus on defense, precision, speed, or power, you have to be trained by one school or another, and different schools tend to attract different sorts of people. People in the Power school tend to be mean and nasty more often than people in the Defense school, but that doesn't rule out a fine upstanding chivalric guy training in that school (if the training doesn't turn him off.)
Anyway, what I meant to say when I started out is this: on the one hand, DMs need to make sure they keep their eyes open to the fact that you *can* change how all of these things work to suit their own idea of alignment. At the same time, I'd rather see WotC release "strong-alignment" rulesets like this with at least a page suggesting how it can be adapted to a weaker alignment system. Otherwise, it complicates alignments even more... and alignments are already one of the murkiest parts of the rules system.
