Since the very first guiding principle of this Remixing effort is fitting the setting into a new system, which already existed and which was designed specifically to represent another vaguely D&D-like setting, albeit one much more old-fashioned sword & sorcery flavored and with a significantly higher level of darker, Van Helsing or Warhammer-like tone, there are a number of things that must change about Eberron to make it fit. There are also some other things that I'm changing not because I have to to make them fit into the system, but because I want to. Most of those are detailed in the additional guiding principles at a high level, but we'll see how they make their way into practice as we go through some of the changes.
Let me first detail the three high level things that are being changed to fit into the ruleset: First, there will be significant changes to the racial spread across the setting for the "demihuman" races, as well as significant increase in the percentage of non-demihuman, i.e., regular human people generally. The setting is much more humano-centric than Eberron as printed, and the demihumans that I do have are truly demihumans, not "photogenic non-humans", which seems to be how Gary Gygax used the term. A demihuman is someone who is human, but touched with a small bit of foreign, and supernatural admixture to make them a bit exotic. An elf, dwarf or halfling is not really a demihuman, although Gygax called them such, because they are simply non-humans. The only non-humans in the ruleset I'm adapting Eberron to are orcs and goblins (at least as playable races); the rest are all demihumans in the truest, not the Gygaxian sense of the word. That means elves, dwarves, halflings, gnomes, hobgoblins, etc. all have to be reskinned as something else, and a number of other changes are having to be made as well. Even more interesting to work into is that the races from Dark Fantasy X actually have their own history and unique origin. I'm not going to abandon this even though this is a different setting, which will have some interesting implications down the line for Eberron Remixed. If the Atlanteans are the descendants of escaped slaves and refugees from Atlantis, the most evil empire ever known, then that's got implications for their inclusion in Eberron and the races that they will end up taking the place of in the setting, for instance. Each of the countries, when I go through them, will have dramatically revised racial percentage breakdowns.
The second big issue that will drive significant change is the magic system. The system that I'm shoe-horning this into also has an older pulp literature based magic system, but it's not Vancian, it's Lovecraftian. This, as you can imagine, will significantly change many aspects of the setting. If magic is much more dark and Lovecraftian and threatens the sanity of those who use it too much, then the notion of more casual wizards running around the setting obviously isn't workable. I've heard a few gamers talk about the Arcanix in Aundair as having a somewhat whimsical Harry Potter-esque feel, but with a Lovecraftian magic, that obviously won't be the case (although certainly the Arcanix will be as carefully hidden as Hogwarts is, albeit for completely different reasons.) I'm still going to accept the low-level magic items conceit of Eberron, done via the Dragonmarked houses artificiers and their dragonmarked access to a different kind of magic. But even the Dragonmarked will flame out relatively young into insanity and possibly death, so one of the Dragonmarked Houses' primary goals is carefully regulating and controlling the Dragonmarked who start to lose their grip on their sanity. All of this presents a much darker vision of Eberron, especially with regards to the magical elements of the setting.
The third big picture change is the monster list. I didn't adjust my monster list at all to make it more "Eberron-friendly" which means that the selection of monsters is a mix of normal vanilla fantasy, classical mythology, and Lovecraftian horrors, mostly, and many of the entries refer to their origin in the Gigantomachy or other classical mythological events. The reality is that Eberron posits various Gigantomachies of sorts; the end of the Age of Dragons doesn't really count, but the end of the Age of Demons does, the end of the Age of Giants, and even the end of the Age of Monsters all have the exact same vibe as a Gigantomachy. I personally think that this is overkill to have so many redundancies in the ancient history, but that's kind of a moot point. I don't know why fantasy fans love really long timelines going back thousands or even tens of thousands of years, but they do. As far as I'm concerned anything that happens more than 1,000 years ago is very ancient history, and very little that happened earlier than a couple centuries ago really has any relevance to what's going on today anymore.
But some of the monsters presented in Eberron will have to be significantly changed. Where Eberron as printed, for example, presupposes that rakshasas are an important element in the Demon Wastes, my ruleset doesn't have any rakshasas, so they will have to be replaced with the Daemons that I do have (and which I prefer anyway.) This will obviously have more impact on countries that are more monster themed than others, like Xen'drik, the Demon Wastes, Droaam, and Darguun, but it will also have more micro-impacts on various NPCs further down the line too.
Anyway, let me make a list of the various things I'll need to talk about. In this, I'll mimic the Table of Contents of the original 3.5 Campaign Setting book and talk briefly about the contents of each chapter, but focus on how they need to change. This isn't meant to be a workable "campaign bible" type of document. The Campaign Setting book is still that. This is just a set of notes and annotations on what needs to change in the campaign bible to make the setting be properly "remixed." In some cases, there won't be much to say about them; there's not really any such thing as a prestige class, for instance, in m20, but I'll still talk about the concept of the classes as presented and if they even still work in the remixed setting or not. I'll even address the included little adventure and how appropriate it still is in the remixed environment.
This is already considerably more in depth than I had originally planned to go; I will not be addressing any additional source material, such as the books on Sharn, or Xen'drik, or whatever. Anything that you may wish to use from any of those books will need to be extrapolated by you based on the principles spelled out here in the annotations to the Campaign Setting document.
Part 3: Heroic Characteristics
Part 9: An Eberron [Remixed] Campaign
A Nice Interactive Map (not maintained by me)