The biggest difference to me, is simply the late swap.
Like topman said above, Draftkings allows Late Swap and Fanduel doesn't.. It's a TREMENDOUS difference in lifestyle.
For me, I like to set my lineups and once kickoff happens, just enjoy the games and my scores. On Fanduel you can do this.
However, on Draftkings, you need to plan around the late swap, even for football. If you have an entry that is in contention to win money, you may have to swap out a certain player to get more or less risky. Top players even plan around this. If you have a certain RB starting on Monday night, it may benefit you to swap him out for a high risk/reward WR (of course if you have the salary left for it).
Also, keep in mind, for NBA, especially, late swap is huge. There will be times a guy is announced as sitting after lineups lock. On Fanduel this could end your night quickly OR it could benefit you greatly if you don't have that player and he has a high % owned.
Late Swap can benefit you and hurt you. But it's something to keep in mind for all sports.