Two factions I've had this happen, the second I appoint a leader for a colony I get a -20 to that leader's loyalty.  Why you might ask...BECAUSE I HAVE TO MANAGE THINGS.  That's the reason given, I'm not kidding.   A leader gives orders, a leader tells people what to do, a leader is a 'MANAGER' that's their job so why would you lose their loyalty, why would you take such a HUGE HIT to loyalty for giving them a job to do what it is that they are trained to do?  What they spend all their lives training and studying to do?  It makes no sense and it hamstrings the player, it's a time sink because it cripples your new colonies and there is no quick remedy or solution so don't try to tell me buy them a gift because -20 is a big hit and a gift won't fix it.    When you have a disloyal leader eventually they rebel on you, if you execute them it costs you big time, it cripples your empire in the beginning of the game it also means if you install any leader with loyalty of less than 80, you're asking for trouble and a loyalty of 60 is borderline.  At 59 it's heading downhill.  

Colonists unhappiness, these people are unhappy at the beginning of the game, it's like you have to have professional clowns to entertain them from cradle to the grave.  It's also a time sink with no easy remedy that doesn't take hours to solve. 

both of these issues are killing the game right out of the gate. Before it's left the gate for good.