Personally, I'm loving Clara. I don't have any problem believing her reactions and I don't find her remotely smug or unphased by things.
She is, to all appearance, a perfectly normal human being with the exception of having a high IQ (and, presumably, an artificially uploaded set of computer skills).
There have been several companions with extremely high IQs (Zoe and Romana spring to mind) and they've been some of my favourites so I have no problem whatsoever with intelligent companions.
For me, the whole mystery thing is something I can just switch off. Whatever it is, Clara isn't any more aware of it than we are so it's not affecting her actions. All of the Doctor's tests show she's a normal human in every way so, to me, that's what she is. I don't expect any kind of a reveal on the mystery until the finale so, until then, I'm not letting it influence my feelings on Clara at all.