The side quests are as much about learning more about the world and its people as they are about anything else. The biggest reason to run side quests is an honest desire to learn more lore about the game. Even the tritest of fetch quests gives you SOME kind of tidbit to learn. If you just don't care about that, give the side quests a pass; they're optional, and not otherwise that important.

That said, the exp gained from side quests is pretty close to what you get by doing MSQs. If you're like me and love every morsel of story I can get my hands on, level two jobs side-by-side, one via MSQ, the other via sidequests. In the latest expansion, I got both PLD and WHM to 80 at roughly the same time by doing this.