First,
Carly wrote:
Molly maybe died and something might have happened at the funeral (Layton turns up and shoots her again/ or gets ran over by funeral car) and gets taken back to 1983.
I am now thinking Molly is all sorts of dead; but there's one problem with the rest of it: Alex isn't back in 2008 at the end of S2. Not really. It's a coma-within-a-coma (DVD commentary confirms this). Chances are, Alex will simply wake back up in 1983.
As for her wearing a lot of black in this coming series: What if it just means she is now completely enveloped in this "alternate world" (for lack of better phrasing), which -- to her -- would be a happier, safer place to be than the modern world?
If you remember Series 1, the Bowie Clown is seen wearing all white (and is a menancing figure). Usually, white represents life; however, if you also recall, Alex's father morphed into the Clown before the bomb exploded and killed him and Caroline. In the context of A2A, white could also represent her modern world -- a world where her parents are long dead, and so is her daughter (in all likelihood); a dead daughter is a reality Alex would not want to accept. It would mean that, in all likelihood, she would have no one waiting for her back in 2008.
On the other hand, Gene wears a lot of dark colours, most notably his black trench coat. Ultimately, Alex comes to believe that Gene is her "constant" -- always there. When she watches her parents' death in 1x08, it is Gene she sees escoring her younger self away, not to mention all the times he has rescued adult!Alex throughout the series. Ray also noted that being/staying with "the Guv" was "the best place to be". In Series 2, Martin Summers is also seen in black; but he starts out as menacing, then becomes downright creepy. Here, I think he's meant to be dressed similarly to Gene because MS is meant to be "the wolf in sheep's clothes" (Gene being the "true" sheep...I know it's a strange metaphor, but it's the best I can come up with right now ;)). The other important bit of Series 2? Alex, at times, is forgetting her modern life.
By Series 3, could it be that she'll have completely forgotten about it, and, as a bit of a side effect (or something), starts wearing a lot of black? (You may also know there's a theory that Gene and co. are also in comas, but they've been in this other world for so long they've forgotten about their past lives.)
Another thing about black itself: Although it represents death, it's also a colour of mystery and power.