I'm considering Either a flute or a guitar
* You'll probably have more occasion to play guitar than flute
* Guitar fills more roles than flute. You can play solo. You can play lead. You can play rhythym. What have you ever seen a flutist do besides sit in the back of the orchestra with a dozen other flutists all playing the same thing?
* Related, if you ever want to jam with anyone or be in any band with friends, you're going to have a much easier time integrating with others playing guitar.
* Playing guitar, it's possible to change your "sound" more easily. Even if you learn on acoustic, you can then pick up an electric and have an entirely different sound.
Guitars have a wide range of sounds, and even a single instrument can produce a very different effect using a neck pickup. If you play flute...you're pretty much playing flute. Sure you can probably adapt easily enough to piccolo or something, but the range of types of sound is very much smaller.
* It's possible to play both melody and harmony together on a guitar because you have five fingers. You can't with flute, because you have only one mouth. Flute makes a poor solo instrument. For example, Watch
this video. He's playing harmony with his thumb and melody with his other fingers. Here's the
same song on flute. She can't do that, so has to put in a CD for harmony and play melody only.
* You're more likely to impress girls with a guitar than a flute
* For that matter, not even just girls. Imagine showing up to a party with your guitar, and playing a couple songs. You could do that. Now imagine showing up to a party with your flute. Are you going to play it?
All that said, I think it's easier to learn to play flute well than to play guitar well. With guitar, it might take a few months even just to get to the point that your fingers stop hurting.