The main story arc in my campaign is about an old royal family(we'll call them the Jones family) who was brutally usurped a long time ago (By the Mason family) trying to retake control of the territory from the Mason family. The players do not yet know much about either of the families (Usurped and currently ruling). Other than the fact that the Mason family usurped the old one (Details not given to players at this point). They learned this when they found an item with the seal of the Jones family on it in a destroyed town. They later went to a cities library to do some research on it. I intend to slowly give the players more information about both ruling families and their motivations. The Mason family is not doing a great job of looking after it's people. (suspicious deaths, poor communication, strong military presence, ignoring raiders plundering traders and heavily taxing the populous.) While this family is not doing anything exceptionally evil they are certainly guilty of doing too little and putting a heavy burden on their citizens. The Jones family has kidnapped the Mason families only heir and is planning to assassinate the king.(Not known to players who abducted the heir yet, other children in the town have also been going missing). The death of the king with no available heir will throw the kingdom into chaos and the Jones family will attempt seize power. However, the Jones family will struggle to assassinate the king and will lose an important family member (daughter) to a failed assassination attempt. This will cause the Jones family to turn to dark magics in an attempt to resurrect their fallen kin and perhaps try to use these powers to raise an undead army and seize their rightful place at the thrown by force.

My players have bought in really heavily so far with little hooks and notes I have given them. They originally banded together to help find the missing prince for money/glory/doing the right thing (different player motivations). I am now looking for ideas to develop my royal family characters on both sides into things they can love/hate/feel conflicted about and I am just looking for ideas/things you have tried and succeeded/struggled with.

Thanks guys and girls! <3

One question I had when I started reading this is "Why did the Mason family feel it was necessary to brutally usurp the Jones family in the first place?"

However, after a bit of thinking, I realized that you could play it like this: 

The Jones family was dabbling in dark magic, but nothing serious. However, this offended the Mason family, who believed that this would only bring about misfortune, trials, and strife on the population. When the Mason family leaders confronted the Jones family about this, the Jones family dismissed their concerns, laughing them out of the castle. Thus, the Mason family overthrew the Jones family to avenge their humiliation and try and prevent the negative consequences they were convinced would come about. Unfortunately, future generations of the Mason family lost some of this zeal, and thus began their less than efficient rule.

This also works with your Jones power grab, in that when they lose the family member, they could turn to "forbidden" dark magics that were much stronger than they were using before to try and bring her back.

even more fun, you could take this approach: History teaches that the Jones family was horrible and oppressive to the populace, and the Mason family were the Resistance Heroes who removed the Jones' from power and saved everyone. This is what the characters have been taught all their lives. Then slowly reveal that the real story is not really in line with what they have been taught. 

Good luck!

I like those ideas, especially the one about the history/real history of the family. The early dark magic will explain away some pseudo plot holes as well.