why does the timer go down when you are watching your opponents last move? shouldn't it start counting from the start of your turn? When there's alot of units around it can take a huge chunk out of your time. (Bug or intentional?)

Otherwise you can press pause at the end of opponent's replay and think about your turn without any time-limit.

u can do that anyway, just before u run out of time, quit to menu then go into it again? You don't lose time watching your opponent when u r both in a game so why should u lose time wathcing him when just u r in a game? seems unfair.

I concur.

I thought developers were planning to prevent that.
Seems hard to me, because I want to be able to quit the game whenever I like.. maybe something like not being able to replay the game you just quited for an hour or so?

They're removing it post-beta.

Removing what?

The ability to exit the turn and regain the time.

What happens if I quit to the menu because some player comes online and I want to play a game with him/her.. Do I get heu less time when I start the first game again let's say the next day?

The timer resets (as does everything you've done that turn). So if you find you are running out of time you can just quit and start the turn again.
This is going to be change in a patch.

No, you'd get full time. It's being removed post-beta.