I rarely use published settings for stuff (I prefer to homebrew my own) but when I do, I prefer to stick to what the books say. I don't necessarily mind changes, but it depends on the reasons behind the changes.

Good reason: I don't like the Spellplague and I am retconing it so that it never happened.

Another good reason: Eberron's Tiamat is a very poor explanation for why dragons don't just take over the world (though it is better than the "They're just too lazy and content to sit on their piles of gold to even try" that most settings use), and I think I have a much better alternative explanation.

Bad reason: One of my players wants to be a Tiefling and Tiefling's don't exist? Let's just add this huge additional continent with a Tiefling empire that he comes from...

Even worse reason: My players know this setting inside and out! Time to switch things up so I can catch 'em off guard!