We haven't discussed conversation skills as much as reputation mechanics. To me, conversation is one of the primary means players have of defining the type of person they are playing in the world. Instead of a heavy emphasis on conversation skills, I would rather allow players to behave in a variety of ways and develop robust reputation systems to react to those choices throughout the game. I think it's more interesting to allow a person to select diplomatic responses and develop a reputation for being a diplomat than to level up a Diplomacy skill and pick the Diplomacy option when it's unlocked for you.
I think some of the best role-playing experiences come from expressing your character's personality in the way that you want and seeing how the world reacts to it. I believe that we can make a conversation system that allows people to do this with dialogues and characters in a natural way.
I'd like to marginalize the speech skills into the dust bin, personally. I think the player's conversation choices should be important without dead-ending quests and I think that Alpha Protocol managed to find ways to do that. There are certainly optimal choices for the player to make if you want a certain type of outcome (e.g. impressing one character instead of another), but dialogue isn't a right/wrong puzzle.
I don't think it's correct to say that I want dialogue choices to be flavor only. I want the player's choices from node to node to actually be more mechanically significant that they have been in most RPGs. That consists of two parts: the immediate reaction within the conversation and the long-term effects of how that choice feeds into your reputation. Sometimes the short-term effects are minor, but the reputation system won't "forget" what you've done.