"Lois" nearly died both days because SHE was the one destined to die. Both times, she's the first one in danger and she's the first one rescued. When she ended up saved, it was like a process of elimination and then Lana was next - fate already setting her up on that road.  This seems to have some backing as when Clark says it's not Lana's fate to die, Jor-El doesn't disagree and as we know from Hereafter, Clark can alter destiny to a certain degree but even he has limits. 

Each time fate is denied, the stakes raise.  It starts with his pseudo-sister.  Then it goes both times to his current girlfriend whom he's about to break up with.   Then it goes to his father with heart problems.  Each person grows closer to Clark, each one becoming more involved in his current life, culminating in the death of his adoptive father.  The one death that both time he missed the warning signs of.

One would think that, as possibly a sign of the future, that none of the people who play a pivotal part in Clark's destiny would be harmed or nearly die.  After all, while fate is going to take it's pound of flesh for restoring his powers, it can't possibly target anyone who is vital to the future to take it from.  And then one think about the people those people who are most important Clark's destiny, to his future. By important I mean those  integral parts and players of the future that, if were dead and gone, it wouldn't be the Superman story we know and love.

The Chosen to Perish:

Lana Lang:  In L&C lore, Lana was pretty much non-existent, until, in the third season episode "Tempest Anyone?", Lois somehow got zapped into an alternate universe where Clark wasn't Superman, and was engaged to Lana. Lana seemed to only appear on L&C in that alternate universe. She was only briefly mentioned in the main universe. In comics lore, she's there, mainly in the background, but she doesn't have much to do with Clark finding his destiny. She ends up married to Pete Ross for a while (who, well, in the comics universe, is a VERY different Pete from the one we've seen on Smallville), and Pete is vice-president to Lex, making Lana the second lady.  Her place in the comics is that of the past - of whom Clark was as a teen, and of Smallville.  She's the girl he leaves behind.  In Smallville, they were on the verge of breaking up in this episode thus finally closing her chapters in Clark's life.

Jonathan Kent:. We all love Jonathan, but... in all honesty, in some ways, Martha's role in Clark's future is seemingly a little more important. On L&C, she makes the suit, and helps Clark with all that, and Jonathan sort of  just sits on the sidelines and nods, and basically tells Clark that being Superman is a good idea.  In the comics, Jonathan serves more of the role he did on Smallville, Clark's moral guide when Clark himself is confused and unsure.  In the recent JLA 0 they even reveal that Jonathan's time is coming in the comic universe; in earlier ages both Martha and Jonathan died.   In movie lore, we all know that he did die, as he did on Smallville, and in some ways, his ghost played a part in Clark's destiny.  However, this influence isn't very great because you never hear him mention Jonathan for the remainder of the film, and he continually refers to Jor-El as his father. I think for Smallville lore, though, I speculate that they're going to make it so that Jonathan's spirit is a guiding force.

"Lois Lane". If she was really, truly Clark's soul mate, would she have nearly died along with the two people that wouldn't be as important to Clark's destiny?  Would fate even target her - and do so before the girl he loves enough to marry, or the father he's known his entire life?  Um... no. I think not. She would have been safe, like Martha and Lex.  Instead, she is always the first pick and very nearly dies in the second timeline anyway.

Those Who Were Saved

Lex Luthor: He's one of the most important elements in Clark's destiny, obviously. He's known as Superman's mortal enemy, and we know it. Lex was not harmed and did not encounter death at all in Reckoning. He caused Lana's crash, sure, but nothing happened to him; Lex always was a safe distance behind, and he always saw the bus - even though he was drunk during the entire driving incident and hasn't always been able to keep his cars on the road (ie Pilot).

Martha Kent: Then we have Martha. In comic and Lois & Clark lore, she was the one who made Clark's Superman suit.  She created the entire thing herself.  That would make her VERY important to the story. (Although, if they do go along with the rumors I've heard about Martha and Clark becoming at odds this next season, that thought may end up crap and he may make the suit himself, like he did in the movie.)   In the movies, Martha is still around and still in a very close relationship with her son as well.  Martha was not  near death at any point in the episode, either.

Lionel Luthor:  Lionel wasn't hurt, either, and though I doubt the character will still be around when Clark becomes Superman (due to his age, his relationship with Lex, and harboring Jor-El), he has become important to Clark's destiny by being Jor-El's vessel.  At the time of Reckoning he still had a job to do; he had to get the warnings about Zod for the season finale and protect Clark's secret from the blackmailer.  Both of which were huge to preserving Clark's destiny, which is what he claims to want to do.

Chloe Sullivan: And last but not least, we have Chloe.  The "non" canon girl who somehow was saved with the Big Villain, the Mother Figure, and Jor-El's Oracle.   She's The Reporter at the Daily Planet. His sidekick in seeking out Truth and Justice. His confidant, his secret keeper - the only non-Kent who knows.  She the woman who's madly in love with him. She was probably the furthest from nearly dying than any of the rest; the first time she's not at the party to our knowledge, the second she's safe at the Talon.  Why, oh, why could this be?  As far as I can tell, there is only reason:  like Lex, even like Clark (which is why his powers were returned), she's got a destiny.  One that is tied directly to Clark and to the Superman story.