Vigil made sense. It would make sense for the protheans to leave behind warnings for future generations (such as the beacons, Vigil and Vendetta)
Star Child just raised too many questions. For example, if he controlled the Reapers and was on the Citadel why were Sovereign or the Keepers even necessary? Why couldn't he activate the Citadel itself? Where did the blue/red pillars come from? If those were built on the Crucible, fine, but they weren't, they were on the Citadel in a location where no organic had ever been before. Why would the Reapers build a control or kill switch into the Citadel?
I do love the ending with the extended cut, with the exception of the star child. Star child just doesn't work for me.
Vigil on the other hand fit the story and made sense.