Jetta TDI doesn't compete with the Sonata, the Accord, Camry, Altima, etc. do.
Take a look at what the direct competition of the Sonata offers in terms of power, fuel economy, standard equipment, technology advancements, etc, etc. You think Honda will be able to stay stagnant and keep their current engine as it is for the next generation of the Accord? Of course not... the Sonata is already beating it in sales in North America, Honda HAS to improve their car. Same goes to Camry, etc. Five speed automatics are a thing of the past in this segment... it has to be 6 speed or CVT. If not, you look outdated, and your fuel economy numbers suffer for it.
I'm not saying anything bad about the Jetta TDI... I'm just saying the Sonata was a much more meaningful entry in the mid-size segment than the Jetta was. The only explanation that makes sense to me is, like Siraqua said, Hyundai's decision to enter the Limited trim instead of the GLS...