So many reasons I don't understand/like this couple and I've written a lot about this in other places, but never here, so...yeah :)
In 1864, Stefan didn't really know who Katherine was. He didn't know she was a killer, that she manipulated he and his brother, whether it was in the purpose of taking away a person's judgment or just having her cake and eating it too. If he didn't know about Katherine's flaws, how could he be in pag-ibig with her? How could he know she was an angel, or anything, for that matter, when he was shielded from it all?
I know people have sinabi that the reason Katherine was in pag-ibig with Stefan was that she was an “angel” as a human and he saw that in her, but I have to point out exactly who she is behind closed doors. No one is perfect – and I've met some pretty angelic people – and I don't hold Katherine to the standards that many hold Elena to. That said, Katherine is not an angel sa pamamagitan ng any sense of the word. She has flaws (and I think they're damn brilliant, honestly) and those flaws are apart of who she is now. Why in the world would you want a relationship with someone that will never pag-ibig you for who you are?
The statement that Katherine has come back for Stefan has barely been acknowledged at all. Katherine says she loves him, but when she has the house alone with Stefan and Damon, you can see from 2x16 that Stefan is the last thing on her mind – even though he is in the house and unoccupied. She claims she's come back for him, but her “seduction” of him? She breaks SE up once and, after that, the ipakita never demonstrates Katherine trying again, or even trying to persuade Stefan to doubt Elena/seduce him. The two episodes that have Stefan/Katherine motivations are Memory Lane and sa pamamagitan ng The Light of the Moon and, as far as seduction goes, are basically limited to dreams.
Not to mention, after so many years of knowing Stefan was alive and never contacting him or letting him know, Katherine came back, first and foremost, for Klaus' little sacrifice. Just saying.
And, finally, if Ripper!Stefan is going to be a huge part of the susunod season (fingers crossed) then I really don't get how these two make sense; it's like Katherine's comment about how Stefan plays rougher (and she seems to like this fact) but her being "touched" sa pamamagitan ng his gentleness and sweetness. Either she loves Stefan for who he is - not the fact that he's turned off his emotions/humanity, for example – or for the ripper she wants him to be. She can't expect both, especially if she puts madami effort into seducing Stefan at his worst than she did when he was at his best.
THIS. SHIP. MAKES. NO. SENSE.