Reading over both of the Mystique collections (one written by Brain K. Vaughn, the other by Sean McKeever), it's hard not to be impressed by Mystique's instincts for self-preservation. She's really quite impressive at turning a situation to her advantage, even if only briefly. Whether it's taking the appearance of a child to try and make those arresting officers pause, or send Rogue into a fury by saying she only wanted what's best for her (because it's better to have a pissed off Rogue trying to kill you than a calm Wolverine, apparently).
The flipside to that is it makes it kind of hard to root for her. Both BKV and McKeever go the same route Ennis did with the Punisher, presenting her opponents who were such remarkable examples of human fertilizer Mystique could look almost good by comparison. Even so, because much of what Mystique does is so clearly self-serving, and since she isn't really in this situation of being a secret agent for Xavier by choice, I tend to find her motives suspect. I'm always wondering what she's getting out of it.
Mind you, it can still be highly entertaining, because there's benefit in the short-term and the long-term, and Raven Darkholme knows the difference between the two and how to weigh it. But again, that makes it that much harder to trust anything she does. Even when Fantomex just happens to show up in time to warn Forge that Mystique is nearby planning to kill Xavier, you know it's all part of some larger scheme, where the potential payoff is worth having all the X-folks out for her blood.
Still, have to be impressed with her commitment to survival. I wonder how interconnected that and her mutant abilities are. If she was always like this, focused on protecting herself, shapeshifting would be a good mutation to develop. The ability to look like anyone she pleases, letting her get close to anyone she wants, or elude nearly anyone she likes.