Admittedly, even when she does become a skilled, level-headed, capable agent, she still demonstrates the same recklessness and ill-fit with the lawful nature of working for a large organization (which causes her to, more than once, butt heads with Coulson as Director due to secrets he's keeping or due to her priorities: examples of this include pressing Coulson for answers about what he's hiding, getting off task and focusing on her family instead of Ward's during interrogation to such an extent that Coulson felt compelled to intervene, and charging off after her father when Raina announced he was nearby). While Coulson indubitably has her faith and she has literally followed him into oblivion more than once on nothing but that faith, unquestioningly following the orders of a "Big Brother" organization as a rule of thumb continues to ill-suit her. Her loyalty to Coulson is based in personal, intimate trust, not a willingness to blindly follow the organization.

On the whole, with regard to her brash behavior and emotional outbursts, she's very much capable of controlling herself and stowing her emotional reactions until a more appropriate time—as evidenced by when she does start to lose her cool when Ward brings up her father, and she excuses herself from the situation to silently (and privately) react. This becomes Skye's M.O. throughout the second season: while she still feels deeply, she controls how and when she presents those emotions rather than attempting to smother them entirely. As she's taken to being tutored by May, one can presume it's with the same intention of using her strong passion to fuel her in a positive way, rather than turning her loose.