Wasn´t she suppose to die shortly after the end of the first game, and that was what made the end a special moment with a emotional bittersweetness, and also made the player action in the last level a moral exercise?

In software development "from scratch" is not a expression you should take at face value. We are always reusing as much code as possible.

However I think ND will have to make their engine more flexible and not as much hardware especifics as the previous one, by the time TLU2 comes out we could have the Pro2.0 or PS5 in the horison. 

Before the reveal they literally said "using an updated version of their engine"

And why will any team build an engine, make one game, then ditch it to make another game all in the same generation. 

And as it stands their engine is one of the best out there.

Either Joel is already dead and it's all in Ellie's head/this is a flashback cutscene as she tries to survive on her own or Joel is going to die towards the end of this game and it ends with Ellie beginning to venture on her own in what is a hint at the third game.

Well, that's what I'm wildly guessing off of this one cutscene. :P

From the panel https://www.twitch.tv/playstation:

• First game was about love, this one is about hate
• You play as Ellie in this game

Few years after the 1st game, Ellie is now 19 years old

They also said that you exclusively control Joel in the 1st game, turned out to be a lie

Hype to the moon and back! This, Uncharted and Mass Effect and Red Dead were the defining game of last gen in my eyes! To see that they are all coming back is a freaking dream come true!

This time Joel is the side kick?

Yeah, just said on the panel that you play as Ellie.

Joels looks to be quite alive from what I saw. I think that they will kill him off after Ellie is ready to stand on her own.