Elfen Lied/WMG

The Woman who took Wanta from Mayu was not his real owner.

 * She was a scam artist who preyed on the homeless, glomming onto whatever valuable or saleable items they might have. Notice how she waited until she and Mayu were alone on the beach, rather than the boardwalk, to confront her, and the fact that Wanta ditched her quickly, with her never seen again once Mayu had a home and protectors who would stop her from just grabbing the dog.

The marriage of Mayu's mother and stepfather dissolved after she left.

 * Targeting Mayu might have been the sole reason he married the mother in the first place. With her gone, the mother was justly left alone.

Chief Kakuzawa knew about Lucy before her capture.

 * The apparent age of  does not seem to match up with a boy who could not, by way of series' events, be more than three or four.

The virus is from outer space and there has been an outbreak before.
Lucy and Sil both gain superhuman powers from a virus, are treated horribly by humanity and so want to Destroy All Humans!, and they are both feared for  Also for some reason a side-effect of the virus is Fan Service.

The Diclonius have a distant alien origin as does the .

 * A British professor of note, Bernard Quatermass, once spoke of horned insectoid Martians who influenced Human evolution in the distant past. They were known for their telekinesis, self-destructive aggression, and the ability to sense who was and was not of their kind, even in Humans who felt their genetic presence. The brief and savage awakening of their influence in modern Humans caused the eventual birth  Another crashed Martian probe like the one found in a proposed London underground station existed in an island off the coast of Kamakura and caused an otherwise wholly Human family to develop

Lucy's Massive spoilers below

 * Think about it.  And after their escape from the facility...well, that's all I've got.
 * All I could say to that is, while a valid notion, to my mind
 * He may be a  That's the point of the "what if," that if she hadn't been so tired of everything Kakuzawa and his ilk did to their kind, the
 * Again, a fair point. One outcome is as likely as another. Perhaps

The two girls that greet Kouta
... ...are Diclonii. Because it would fit with the and they have hair... holding-things in the right place.

Aiko Takada
For most of the manga, Lucy and the viewer are led to believe Aiko Takada. However, during the last chapter of the manga, Wanta walks past a poster for an art exhibit, and the woman on the poster looks like an adult version of Aiko. What's more, the name "Takada Aiko" is written on the poster. This led me to believe two things:
 * Kurama lied to Lucy in order to keep her from looking for her. It's a lot easier to keep a dangerous test subject contained if they have no reason to try to escape and reunite with someone.
 * Since Aiko's "Death" caused Lucy to swear Revenge by Proxy on Kurama, I guess that didn't really do much for him.
 * Since, Kakuzawa probably offered to cover that incident up as long as she stayed quiet and forgot all about what happened in the warehouse.