(Mild spoilers ahead! But mostly just character analysis.)
Burn Notice had a solid midseason premiere last night with "Damned If You Do," and it seems we now know what obsession will replace Michael's quest to find out who burned him: protecting Fiona. For this episode, at least, this also became his priority over saving the world or helping random people, and . . . I think I'm okay with that. It makes the calculus of Michael's decision-making more complex, and therefore makes the character more interesting.
In this show's moral universe, the ends usually justify the means. Michael may hurt people, but he generally thinks he's serving the greater good, even if he's not entirely convinced he himself is good. His constant need to save the world is all the more powerful given that, at least some of the time, he thinks he's a bad person, or at least brings bad things down upon anyone he cares about. Michael has a touch of Josh Lyman syndrome ("He goes through every day worried that somebody he likes is going to die and its going to be his fault. What do you think makes him walk so fast?") but with him, this tends to play out on a larger but more impersonal scale. Sure, saving random strangers (or countries) is great, but it's also a symptom of what Michael says about not letting himself care about individual people.
Now, though, he cares, and everyone knows it. When you move your ex-girlfriend into your apartment, you lose all plausible deniability, both to your mother and to the bad guys out to get either or both of you. He's doing bad things, things that will hurt people, because that's what's necessary to protect Fiona. (And Fiona, as she herself points out, is no damsel in distress, which makes this all the more compelling.) If he were on Vampire Diaries, this is when someone would tell him to be careful - his humanity is showing. And it makes him a much more interesting character. Michael saving the world? Done that. Michael damning the world to save the girl? That's something different.