Any chance that both races could be neutral at start and after some quests we could choose a faction?

No. Blizzard has already stated that they want species to be faction specific.

If the races were to be neutral (which still doesn't seem likely to me), there would have to be something that sticks out between the Horde and Alliance versions of Worgen, for example, to distinguish between them. Nobody wants a Worgen or Goblin near them when they can't tell the difference between friend and foe.

@Owen: You may recall Blizz once said "No" to PVE to PVP transfers. You might remember them saying "No" to Faction Changes. Saying "Blizz said no!" on something is as strong an argument as chain mail made of aluminum foil. They've changed their minds in the past, and will probably change them again in the future.

I wouldn't hold my breath on either side of the speculation. Choosing your Faction would be cool. It would also be confusing in PVP. As far as that goes though, I rarely look at what the model I'm killing looks like. If it's red above it's head it's going to be dead.

The "confusing in PVP" argument has always held little weight for me since I react to the BIG RED LETTERS over a toon's head instead of squinting to see what types of elf ears are poking out of that armor.

Sure, visual distinction is nice, but if the main Blizzard argument against same race in both faction is visual ID in PVP, then I say it's not a very strong argument.