I've been really curious as to what it is that kate did that caused her to be crossed off because i honestly can't think of anything so significant that happened to only her that would cause it... which lead me to think it had something to do with other characters, namely jack:
i've sort of been toying with a theory lately that it might have something to do with jack and potentially his feelings for her. bear with me here:
We know that the whole basis of the show has something to do with love- as seen by the whole au mindwarp stuff and confirmed by Darlton. Hurley is a candidate and he lost the love of his life- Libby. Sawyer is also a candidate and he too lost the love of his life- Juliet. same goes for Sun or Jin- although i think jin is the candidate in this scenario because suns death was inevitable, whereas Jin chose to die. Sayid also lost the love of his life AND Jacob seemed to have something to do with that (distracting sayid while nadia was hit by the car). also perhaps shannon's death is related to Sayid's candidate status- he was getting too close to her so she had to be removed. also helen died in the original timeline.
claire was a candidate and she lost charlie (and one could also say, aaron).
and what about ben- he lost annie (who appears to have been a love interest) aswell as his mother and probably his most significant love- alex.
rousseau's name was also on the wall and her lover died- (granted, she did kill him but he already had "the sickness").
and not sure if Richard was ever a candidate but his wife also died- could be relevant.
what if by falling in love/being in love candidates are unable to fulfill their role as replacements for jacob?
maybe the island needs to ensure that its protector is 100% loyal to it, above all else? john showed this kind of belief and loyalty form the beginning which is why, i think, the island was so communicative with him.so the island needs to kill of this obstacle to ensure its own survival and protection.
and as jack is frontrunner for candidate it makes sense that the island would sacrifice kate's position- she needs to be eliminated (maybe why she was shot) so jack can focus on his true role.
which, if correct- sets the finale up for some love acknowledgement between kate and jack (maybe tied into their "recognition" in the AU, if it happens, which i assume it will). plus if jack finds out that kate is in danger, i think he would always choose her over any loyalty to the island (as we saw when he got on the sub when she was shot). so we could end up with jack protecting kate from island (or potentially jacob/mib have some involvement)- whoever is masterminding this whole thing.
I've always thought that they were making jack being primed as the next candidate so in your face (plus he is the obvious choice) that it won't be him- its too obvious. so my bets are he ends up with kate and someone else takes over.
i realise this contardicts slighlty with the idea that jacob/teh island are "good" and MIB is "bad" but i have serious questions/doubts about jacob and his motives. And i honestly can't see any of our heroes volunteering to spend the rest of their life alone on a desert island. I think being the "new Jacob" is a sacrifice, and to ensure the candidates are willing to make that sacrifice, the island has to take away their reason for being, ie their true love.
I also think this will tie in with the alternate universe- everyone is alive in the AU, and seems to be reuniting with their true love and regaining their "memories"/feelings. I think this pattern will continue for all the characters, maybe because being together is "the way things are supposed to be". I'm still not sure exactly how they're going to tie together the two timelines, but i think it will definitely have something to do with this.