File vs. Scissors?

I would take the file without a doubt.

With a file and a knife I could accomplish the vast majority of tasks I would use scissors for. However, with only a knife and scissors I would have a tough time accomplishing tasks where a file or metal cutting/shaping tools would normally be required.

Basically, the file means I have a better chance of being able to improvise a solution to a specific problem with the multitool. Which, is pretty much the whole idea behind a multitool; it's a compromise of many tools that allows you to possibly improvise a fix. The greater tool variety, the better chance you'll find something you can use.