I haven't read anything past NJO, but as I understand it, Jaina suddenly turning incompetent is more a result Karen Traviss' hatred of Jedi and fetishization of Mandalorians. In Traviss' mind, Jaina Solo, being a Jedi, can't even tie her shoes right unless she's trained by a Mandalorian.
Yeah, basically. God forbid the Jedi be awesome and intelligent people. Also, she starts fawning over Jag apparently instead of being the independent woman we know she should be (esp. as a daughter of Han and Leia).