Yes Man gives you the choices to make in handling the factions rather than just playing Kingmaker to someone else.
He will also tell you long term results if a faction is ignored, I think he does this AFTER you say ignore one.
Save before choosing to ignore.
Spoiler BoS is one which would become a problem given time.
Playing through the House Always Wins line will get you familiar with most factions and why they may or may not be be a prob long term. <-- Hard Save before starting lets ya go back to this point.