They are one in the same. Neither one is really any better than the other. Now there are pros and cons to them both just like anything else. The only real negative with flourite is it needs thorough cleaning, cleaning that most aren't up for. If you clean it, its just as good. I can deal with flourite not coming with bacteria, a tank will eventually cycle. Some like the look of eco better. This is the visual aspect of the two. I find flourite more natural and more attractive. Eco for me has a few negatives, it cost more for less. Eco comes in a 20lb bag in which some of that is liquid. Flourite comes in a 15.7lb bag, all floruite. Eco is lighter. Can be a pain to plant in. Flourite holds plants fairly well. Unless you get eco from petco, it can be more expensive from what I have seen. Eco also has inconsistent grain sizes. Flourite is all the same grain size. I have also heard complaints about eco lately that not all of it is what its suppose to be.
You can't go wrong with either. If you set up two identical tanks with only the substrate being different, you won't see major differences more than likely.