Most if not all of the entrenchment and diplomacy features will be in rebellion.

We dont yet know if you install rebellion with/over diplamacy or if it reqires a seprate install.

If one player is playing rebellion and another player is playing entrenchment they can't play the same game, however the player with rebellion will also be able to play entrenchment and therefor play together.

Mods will almost certainly not be compatible.

System requirements should be about the same, possibly a little more or less depending on features added and optimization's.

I don't think we know that yet.  If someone buys Rebellion and never owned any of the other games he might be limited to playing Rebellion.

at a min, you get all the old content... so if you have rebellion, there is not point to buying the other things if you didnt already have em.

unless you have a friend who is refusing to upgrade for some dumbass reason... in which case you should buy him rebellion, instead of downgrading yourself.

It's not exactly going to be free.  The barrier for someone who owns Diplomacy is $30, and it's $40 bucks for those who just own regular Sins or Entrenchment.  It's conceivable that some casual players might not want to drop that kind of dough on the game even though they have may friends who just bought Rebellion.

If newbies can't work their way up through the earlier versions, one concern might be that Rebellion will be overwhelmingly complex.

Seconded, Zeta1127.
I'd love to see more tutorials on things in Entrenchment and Diplomacy, especially about Starbases and Envoys.