Least I Could Do/WMG

Rayne is perfectly sane for the world in which LICD takes place.
Everyone else just has a hyperactive Weirdness Censor. (The arc where he "hallucinated" a soldier telling him to nerf attack everyone was actually his sleep-deprived state allowing him to see the ghost of a guy who actually was crazy.) How else could you explain people noticing the talking llama?
 * His niece is the same way.

It's been done before...
But you have to admit, everything would make sense if he was either Jack Harkness and/or a Time Lord. Or, if you want to get technical, the child of a Time Lord *and* Jack Harkness. He will never know the truth, or why he has these powers... only that he has them.
 * I prefer to think of him as a male Haruhi.
 * It's Word of God that Jack Harkness has at least one child we haven't been introduced to. You cannot easily convince me that Rayne, who shares his looks and a fair chunk of his personality, is not Jack's kid. (Although isn't one of the strips about Rayne's conception or something? Huh...) Also, remember how Jack once mentioned having got pregnant? Perhaps things get weird around Rayne because he was so directly exposed to Jack's Bad Wolfy stuff for about nine months.

Rayne's love life will go the way of Chobits.
By which I mean that the series has been Cleaning Up Romantic Loose Ends now with Issa  dating someone else. At least in Issa's case, it was with a pre-established character. This will continue until everyone Rayne has actually had feelings for is taken, save for one. Or none, if that vision of the future comes to pass.

The girl from the most recent Beginnings is the one Rayne was crying about in his flashback sequence.
"Have to chase me" "Never going to stop". Huh.

The entire comic is subject to Rayne's Self Serving Memory.
Rayne is, like Scott Pilgrim, remembering the events of his own life in such a way that it makes him look like a perfect amazing sex god, and because he's the protagonist that's how the reader gets to see him. But in reality he's been rejected by most of the women he's been with (except for cases of pity sex), Marcy has him on an extremely short leash due to his horndog behavior and skipping work for the slightest reason, and his friends only hang around him out of a sense of obligation or because they're making sure that he doesn't get himself killed the next time he tries something stupid like making his own Iron Man suit. The delusions have been getting stronger as the series progresses, which is why the comic has seemed to bend even further to Rayne's liking (his friends stopped "whining", he can score even in ludicrous situations, etc).
 * Tying in with the recent storyline, Rayne has clinical depression and the comic is how he wishes reality would be, rather than his being a no-name pencil-pusher who spends all his free time watching sci-fi movies and unsuccessfully trolling for booty.