Hmmm - not sure about the complaints that too much is going on. There's only three main threads - the bloodyface killer, Arden's experiments, and the possession of Sister Sweetie Pie (yea, i forget her name). Everything is is a side story like the ghost stories last season - not the main plot, but interesting nonetheless. If I get a decent resolution to those three topics, I'll be happy.
I see the Aliens as amusing, but not anything central. Perhaps they will give some nod to them by the end for Kit and Grace, but it's not necessary. Wrapping up everything to do with Lana, Kitt and the Doctor is pretty straight forward, since it's all the same story and ties into the modern version of the bloodyface killer.
The ones to root for are obviously Kit and Lana, although I'm quite sure it won't be a traditional happy ending. Then again, it wasn't a traditional happy ending for the family last season, and yet there was some level of satisfaction in what happened.
One of the interesting things about modern horror, as opposed to more traditional (100 years ago and more) horror stories is the need for it turn out good for the main character. It's interesting that we need that now, when once it was pretty rare.
And while the main characters have been great, the guest actors have also been fantastic!