I always see Garcia as being on Emily's side because no matter how much she may be JJ's best friend, she can see that JJ is clearly being a giant idiot about everything.

And I completely agree - I find it so much easier to write Emily than JJ, at least in part because, as you say, it can be pretty difficult to understand JJ's motivation. Because if she was in a relationship with Emily for parts of season three, than also being in a relationship with Will makes her not a very nice person, and seems quite OOC! Plus, I'm just more interested in Emily than JJ.

I forgive you because everyone should watch IPS before they do anything else. Mary McCormack + awesome leather jackets = my favouritest thing ever in the world.