I think now that since both Klaus and Shane want the cure to be found (for different reasons, of course), and both are not stupid and have picked up on the group dynamics they know that (a) Damon is pretty much in charge, but (b) when it comes to not only Damon, but pretty much everyone else in the group, Elena is the unifier -- she is the one person that they all care about. So, it makes perfect sense (and is way less convoluted, well, I thought it was simple but that's because my brain came up with it so it made sense to me, others were all huh, too complicated) that instead of Klaus and Shane directing the sire bond theme, they are rather using it as misdirection. To keep Damon, Elena, Stefan off-balance, to keep Damon, Elena and Stefan wanting to find the cure, both of them -- after hearing about Caroline's theory which she and Stefan decided was fact -- decided to make use of this perfect tool and thus have played along with it.
This fits even more so when you take into account that Shane -- after spending time with Damon the last few days -- realizes that Damon may not want the cure if it means he's going to lose Elena so that's why he's suddenly contradicting himself about Elena's love being real (which he pretty much said to Elena in "O Come, All Ye Faithful"). So, yeah, I still think it's not real and that Shane hypnotized Elena to obey direct commands from Damon or something similar. However, now I think that Klaus and Shane are just taking advantage of this theory and using it to get what they want.
Hopefully we'll see just what is going on before this next batch of episodes ends.