The two major differences I've noticed are the sites pricing and the required roster spots.
Fanduel seems to often take long to adjust player prices. This can result in too many obvious value options (especially if you also play nba contests). On the other hand, DraftKings seems quicker to adjust player prices.
Fanduel requires drafting a kicker, while Draftkings does not and requires a flex.
I like Draftkings side on both of these differences. I feel like the tighter salaries and the flex position help skill prevail. It also leads to less similar lineups. Check this out for more on the differences between the sites https://dfsstrategy.com/sites/