I think when you talk about this version of Civilization which I think attempted to acomplish the same thing the Eagles game version its worth doing a comparison because I believe somehow neither game managed to get it right, but both games did enough right things that when combined (in an imaginary 3rd version) it would be a great game.
Rules wise I think Fantasy Flight games did a considerably (I mean... CONSIDERABLY) better job of laying it out and making it clear. We picked up the Fantasy Flight Version and where playing and talking strategy after less than 20 minutes. It took us 2 full games of the eagle version to make heads or tails of the rules and even to this day their are things we just ruled a certain way because we haven't got a clue what the hell the developer was talking about. In BIG part I believe this is why the Eagle version gets a bad wrap as a game, its actually overall a really great game but getting your head around the rules which actually are very simple, but made overly complicated by a terrible rule book has put off a lot of people.
As for mechanics, the thing that kind of puts me off a little bit about the Fantasy Flight version is that its a bit too abstract for me in certain places. The whole combat system is very quirky and just doesn't really give you the feel of an ongoing war. Its more like "a battle takes place" than its over and will be over for a while because its going to take you several turns before you can get back on your feat. Their is very little tactical combat, or strategic planning. Its move across the board to an obvious destination and have a battle for which you can guestimate the results pretty definitivly simply by paying attention to what people are buying. There are no suprise attacks, or borders to dispute. Its almost like they could have removed the map all together to be honest. I really don't care for the combat and combat really should be a big part of a civilization board game, I mean civilization the PC game is at least 50% combat if not considerably more.
I like how they handled city management in both games, their is a certain amount of abstraction that has to go into this (its so even in the PC game) so I liked both systems equally. I also liked the cultural track in the FFG version, I thought that was a very clever way to handle culture as a concept in a board game.
My biggest beef and probobly the primary reason we play the FFG version over the eagles version play length. I love long games but the Eagles version can exceed 8 hours easily and I found that quite often the ending is very anticlimatic because its not uncommon for a player to kind of run away with it in the end. I think making a Civ board game and finding a way to confine it to 3 hours is an awsome feature and while we have no issue with long games per say, its often more fun to thing of board game nights as "hey lets play some board games" rather than "hey lets play civilization and hope we finish!".
One constant complain about the FFG version I get form my group is that the civilizations themselves are kind of narrow minded in their approach to game victory. They are so obviously designed to go for a very specific type of victory that its foolish to attempt something else, and so as the game starts we know what victory people will go for based on what civilization they ended up with. I think it would have been better if the game was more dynamic and we sometimes play the civilizations as "blank" with no abilities.
Overall though assuming we have the time we still prefer the Eagle games version noting that we have created a lot of custom house rules and presuming that we have dedicated a game evening to play just that one game. Despite that though we tend to play the FFG version more often.