The NEX-5N has a higher ISO 25,600, a touchscreen LCD panel (with object tracking) that can tilt up or down, AVCHD 1080P 60FPS, has ISO 100, continous shooting at 10 FPS, and is thinner. Also comes with a portable flash, but I rarely use it.
The NEX-F3 has a built-in flash and has a slightly better battery life compared to the NEX-5N, but that's pretty much it. The lowest ISO it has is 200, it's thicker, no touchscreen LCD panel (no object tracking), the LCD panel can only tilt one way, slower continous shooting at 5.5 FPS, etc.
NEX-5N is hands-down the better camera. The NEX-F3 is an improvement over the NEX-C3 for sure though.