I've not run a lot of missions, but I can tell you the cons of org play in general (I've run something like 180 Pathfinder Society games):
1) Rules Flexibility: A new splat book comes out with terrible balance? If it's allowed in missions, it's allowed at your table. If some archetype gets hit by the nerf bat in a way you consider too harsh, you have to go by the new ruling. If you really liked the way 4e or even 3e and earlier handled something, but there is a new rule you think is worse, you're stuck with the new rule.
This inflexibility is necessary in order to provide somewhat consistent play across tables (since, especially at a con, I could have 6+ GMs for one character), but it can be stifling to someone used to the freedom of tabletop home games.
2) Time constraints: yes, adventures are designed to fit their time blocks, but players often don't care about your silly pacing concerns. You might have to rush certain points, or move along past what was becoming an interesting roleplaying encounter. This is most apparent at conventions, where the time limits are often much less flexible (someone else will need that table in half an hour, you really can't go over time). At a store, depending on scheduling, you have more freedom to exceed the time limit, but convention GMing is an art with a skillset all its own.
3) You cannot tailor your story to the players, they have to tailor their characters to the story. Some players, especially newbies, might want more. Especially if they're used to GMs tailoring their home games to character backstories. There are missions contacts and hints as to where things might be going, but if the player's are to get the benefit of these story connections, they will have to be the ones to grab those.
All that being said, I love convention GMing and org play GMing in general. I'm one heck of a better GM than I was before I started doing PFS (my first org play experience). You'll see how other tables deal with corner case rules, how to keep the action moving without getting bogged down in a rules debate, and you'll meet a heck of a lot of awesome people. True, not all convention-goers and store walk-ins are wonderful human beings, but I've had far, far more positive tables than negative. It can also take the pressure off you, once some of your regulars are willing to step up and try their hand at GMing (though that can take awhile). Org play means you don't have to do all the work, and can even get a chance to be a player now and then.