I really doubt that it's going to be Lionel, judging by the look on Clark's face in the teaser commercials. When he crouches and crumbles the dirt on the grave, it's too intimate to be someone that is a lesser player in his life. Like I have said, it's either Jonathan or Chloe. Jonathan because that's what happened in the movie, and Chloe because she isn't a major character in Clark's future unless she changes her name to "Cat Grant" or whatever that chick's name is.
Chloe is kind of an unlikely factor, because in the vampire episode this season, at the end she said that Metropolis was the home of future superheroes. How would she know that Clark would become a hero later in his life if she dies? It could be argued that she's refering to a future episode featuring a female superhero, but that's still after 100. Another argument could be that she was being an omniscient narrator, which I can't deny.
Anyway, I'm lead to the conclusion that Jonathan Kent will die. I have read no spoilers to this effect, it's just a guess on my part.