The 3 alliances are completely separate at all times, they are enemies, you do not talk or trade, you attack before they attack you, this is what has been done before and it works very well, you always know who your enemy is. It also gives you a sense of pride for your alliance and a sense to protect your lands from enemies. Nothing is stopping you from creating charcters on the same side as your friends, you can always be togeather. While playing you will never know your enemy so you will Never becomes friends to not be able to play with them.
They made it so you could do the other alliance lands just so there was more PVE content to do. This is making the content 3x more than origionally. Aside from the main endgame which is Cyrodiil