Will there be a mechanic for switching from hero to villain or vice versa?
No. You make the choice of hero or villain at character creation, and it can't be changed after that. This is so it is clear to other players in PvP who is on what team.
Will current storylines in the DC comic universe affect the MMO?
The game will launch "pristine"; that is, the DC Universe in the game will be the popular, well-known one. Wonder Woman will be in her classic costume; Bruce Wayne will be Batman; etc. From there, storylines from the comics may start altering the MMO universe, but at least from the get-go, the game will start with a clean slate.
DCUO will be getting its own bi-weekly comic as well.