Is there anything about these books which you didn't like, or where you could see room for improvement in terms of overall presentation and/or structure?
Okay, I'll try to answer that. For the FRCS and ECS, I'm working off memory, while I haven't finished the Pathfinder book yet, so the answer will be necessarily incomplete.
FRCS (3e): Ironically, the biggest strength of this book is also its big weakness. Because the font size is so small, and there is so much information packed in there, it took me a long time to read and assimilate all that information. It also remains hard to find things quickly, a significant weakness when running the game at the table.
The other criticisms I have of the book are to do with content - I'm not really a fan of FR.
Eberron: I may be mis-remembering, but I seem to recall that this book didn't come with a poster map of the setting, and that that came with Dragon later. If correct, this strikes me as a rather terrible omission. Almost unacceptable.
However, two things I did particularly like about that book: right at the start, there is a list of ten key truths about the setting, which did a really good job of setting the tone of the whole. Also, the full-page artwork between chapters was particularly good, again setting the tone of the book very well.
Pathfinder: Three things leap out at me, all from the chapter on the nations of the setting (which is as far as I've gotten). The first is that it sometimes feels a bit like a "tick-box" world design - there's the Egypt-analogue, the Viking-land, the Barrier Peaks equivalent, the devil-ruled nation, the demon-ruined land, the Pirate-city, and so on and so forth. It's well written, and probably does all this by design, but that was the sense I got from it.
Secondly, I think the book maybe tries to cover too much in too little space. There is a distinct feeling that a great deal has been glossed over. Although, oddly, I suspect it covers a lot less than the FRCS, and may well spend a greater word-count on each nation (on average). Perhaps its an artifact of this being a new world while FR is twenty+ years old - the FRCS thus gives the impression of distilling all that accumulated lore, while PF just presents most of what exists.
Thirdly, the nations are presented in strict alphabetical order, which means they tend to jump around the map. I think I would have preferred that they divide the map into regions, and discussed the nations in regional areas of about six or so. They would also have benefitted from diagrams showing (in brief) the relationships between the various nations. (Of course, this would mean cutting something else. My vote is for the Prestige Classes, because, frankly, we have enough by now.)
General: One thing that has occurred to me recently concerns the presentation of the history of the world. Typically, this is given a chapter in the book, quite late on, and starts at the creation of the world, covers a bunch of legends, and then deals with recent history briefly at the end. This makes a certain sense, in that it's all done chronologically (as does presenting nations alphabetically), but I also think it's sub-optimal.
The thing is, the recent history of the world is generally the most important part. And, in fact, it goes a long way towards setting the scene for the current state of the world. As such, I wonder if perhaps that should not only be presented before the ancient history of the world, but should in fact be divorced from the history chapter entirely, and instead presented in the introduction/overview section of the world, or even at the start of the chapter detailing the nations of the world.