In my personal opinion, it's far too early to pass judgment on the 2006 Sonata. The issues I've seen seem to be more related to assembly than part quality, so I think that reflects Hyundai's continued commitment to quality. Once upon a time, part quality was horrible.
But both of the engines in the 2006 Sonata are new engines, so there's little data to make conclusions. My general impression of Hyundai is that they've improved their quality dramatically, especially in the first few years/30k miles of ownership, but I'm less convinced over a significantly longer haul. I'd still give the nod to the likes of Honda and Toyota (certain particular models excepted) over the long haul.