I am thinking of starting a 3 player campaign... I have bought 2 core sets atm and I am thinking to focus in one sphere for each player. Is it possible? I heard from a friend of mine that we will have great disadvantage in later expansions...

any opinions?

I don't know a lot about the quests from the campaign, but playing 3 mono-sphere decks is certainly a option in general. Keep in mind though, that certain traits have powerful synergies. For example the hobbits heroes you get in the Black Riders work best if you play all of them together.