Although certainly not exclusively a "mature" theme, the concept of betrayal and manipulation is something I'd love to see explored -- and I think Obsidian could really pave the way to portray a betrayal of the player character that may really hit the player. To an extent a great deal of CRPGS had ideas of betrayal and incidents in it in their games, and KotOR II really made an interesting theme out of it; but at best those examples (although by far a lot more intelligent than the content of other games) were not precisely an innovative or world-changing in their application or handling.
In Eternity Obsidian could break new ground by having companions have their own motivations and ideals that they won't just put aside for the player: they may be nationalists for nation X, want to change Y, believe in Z, and so on. If the player disagrees with them or goes against those ideals, there should be more than just a sudden dialogue where the companion argues with the PC and they leave/fight you unless you pass a speech check (although this is something that isn't necessarily bad), but companions potentially seemingly liking and working with the player while working against them in an attempt to further their own beliefs and interests: plots that may be subtly conducted, but potentially only picked up when it could be too late. All the while companions could be working against the player; perhaps there could be an unseen debuff in combat when a companion is working against the PC to try to get them hurt, and perhaps dialogue trees could open up to completely new avenues as characters lie to the PC to help further their plot.
Here's an example of something like this (a very extreme one, but it gets the concept along well). A companion with the PC has discovered that they will not support their cause that they back, this companion, a woman, seeks to try to ensure that the PC can no longer challenge their beliefs. They attempt to manipulate the PC into beginning a relationship with them, and if the PC accepts, they act as though they are in love; seducing them, etc. Eventually the party reaches the Companion's city, where the player denied the companion's cause. The PC may support their companion's cause now that they're romantically involved with them, the manipulation non-violently paying off for the companion; but if the player still does not support the companion's cause, the companion could give away vital information to parties who want the PC dead: intimate information that makes the PC very vulnerable gained from the false romance. The ambush would potentially scar and nearly kill the player, and the companion may or may not try to kill the player to. Whatever happens, the player finds out the betrayal; fostering a great deal of role-play, and making the story and characters very dynamic and multi-dimensional, and adding a lot of replay value.