Elena is Katherine.
Elena looks exactly like an immortal vampire from the 1860s, and survived a car crash that killed both her parents. The simplest explanation is that she actually is the vampire, and "Elena" is just her cover identity. As for the sun, maybe she just has an earring that protects her. Matt is doomed.
The show doesn't hesitate to kill of supporting cast members and likes a body count for finales. Matt thinks that Caroline killed his sister, which makes him rife for being used by any number of villians, and he doesn't serve much of a role on the show other than being Caroline's love interest. He's got Alas, Poor Scrappy written all over him. Alternately, Bonnie is doomed.
The show has gone two seasons and failed to do anything with Bonnie. Matt could at least fill a Xander-esque role as the only real Normal on the show and now that his sister is back, he will probably get some more interesting storylines. While Bonnie on the other hand has even less of a character than Matt, and it seems like she will be sidelined in her own romance storyline what with the return of Anna and Vicki. Plus, her new powers have made her Too Useful To Use, as she is basically a walking Deus ex Machina now and so the show runs the risk of relying on her too much to easily solve plots. Alas, Poor Scrappy is more or less the only option left for her. Either way, the show is bound to kill off another main character sooner or later, and Matt and Bonnie seem to be the most likely candidates. In order to defeat Klaus...
Elena and co will revive all of the Orginal family. Elena will obviously try to rescue Stefan, and will realise that she doesn't have the firepower to even hope to touch Klaus. So she will track down Elijah (probably using Bonnie's tracking spell - remember Bonnie needed Elena's brother's blood to find her, and now they have Klaus' (Elijah's brother) blood). Elijah is buried along with the rest of his family, so when he wakes up he will then revive all his brothers and sisters. Cue 6-on-1 Orginal-Vampire sneak attack. Lexi is an Original.
Because:- A) She is so popular that the writers will want to bring her back, and flashbacks alone aren't enough for that.
- B) It would be awesome.
Elena will end up with an Third-Option Love Interest.
Just to make the shippers squirm.