FanFiction and Wattpad are both sites for writing Fanfiction, however, that is one of the only things they have in common. FanFiction is for that alone, writing fanfics however if you wanted to upload your own work you’d have to go to it’s sister site Fictionpress. Wattpad allows you to do both without having to leave for a different site.
Another difference between the two is that FanFiction is well organized and everything is easy to find as well as being easy to navigate your way through the site. Wattpad however is not as easy, with both fanfictions and original work appearing on the same page it can make it hard to find a story you want to read or even the category you were looking for.
And while I have belonged to FanFiction longer than I have belonged to Wattpad I still find things I like about Wattpad more than Fanfiction such as the ability to type a story on the site itself and keep it there and then publish it later. You don’t have to upload a document to publish a story. Also Wattpad gives you the ability to bookmark the page you left off on, something Fanfiction can’t do.
Also many editors and publishing companies are rumored to watch Wattpad for upcoming, inspiring authors. There are no rumors like that FanFiction.
Despite all the things Wattpad has that would make it seem better than FanFiction, I still find myself drawn to FanFiction than Wattpad. Wattpad’s lack of organization and selections are a big hit to it. Though if you ask anyone the site you start writing on is noramlly the site you lean in favor towards.
jevans11blog 
I think it’s interesting that publishers are watching fanfiction sites. If they want to stay in business, this is probably a good idea, given the vast wealth that is to be gained, apparently, by finding that one writer in a million! I also wonder if this is the future of literary publishing. There’s no reason why publishers shouldn’t also be paying attention to blogs, for example, where a lot of good writing exists but remains undiscovered.
Watching blogs isn’t a bad idea and publishing companies would be surprised to find the different kind of writers on here as they would anywhere else. By opening up a wider range of writing skills publishing companies would in turn be able to explained on their business and probably wouldn’t have such a hard time finding good writers.