I don't remember Regal description right now but maybe they don't need to be exclusive. What I really mean is that there could be cases where it would make sense that you can have at the sae time some mertis and flaws that form a "value/effect" point of view contradict each other. If you picked Totally Blind, you shouldn't be able to pick Eagle Eyes. But picking Hated shoudn't prevent you from picking Royal Blood.
About costs... not sure. Weaknesses shouldn't just be a "Point Source". If they don't have true drawbacks, low point score would be fine (but merits should also have a low point cost if they don't really give "meat"). But if they have some real drawbacks, increase the point value! Maybe picking Ancestral Blood Feud for 5 points wasn't such a good idea at Sovereign creation now that you have to deal with constant attacks by an NPC faction and his unaligned allies, but Unfriendly Face for 1 point wasn't that bad deal as it only has a slight penalty to diplomacy.
(names and point values on the fly)