I chose "Play both, prefer missions", mainly cause the options were so limited.
I actually don;t get to play much of anything these days. I play a handful of SR games here at home each yer, and I play a few Missions Games at cons. And that's about it :/ Mostly, it's a time, energy, and available group that wants to play issue.
But for my money, I love both, and both have their place. My "Home games" are nice for that "I can do whatever I want" feeling. But Missions games are also a blast, for many reasons.
One, because they hearken back to the days of SR1 and 2, and that feeling of a Shared World. It's a lot of fun to swap stories with other "old vets", discussing what you did in Mecurial, or Missing Blood/UB, or Harlequin.
Two, because it's kinda cool to be a part of the "Official" game. When you play Missions, you know you're actually involved with something that's a direct outgrowth of the official Shadowrun books, and there's always that chance that something you do could have a real, lasting impact on the Shadowrun world down the line (a small chance, granted. Just like a real Shadowrunner!

).
THree, because sometimes it's nice to have a prefab campaign to play in or work with.

Like I said, I love my home games. I love the freedom to do what I want, change what I want, and over the years I've done some crazy, very non-canon things in my games. But both have their place. Both serve an important purpose, and I'm glad to see both existing.