Seeing you talk about advantages/disadvantages reminded me that I wanted to talk about those things before, but I have been so busy with other things I completely dropped the ball. So, I'll gladly take this as an opportunity to pick up the thread again!
If I'm thinking of them correctly, advantages/disadvantages are somewhat like perks that are selected at character creation, have overarching effects, and can be beneficial, detrimental, or some mix of both. In many cases, they help to enhance customization and/or roleplaying as they can define a character in ways that extend beyond attributes or skills. So, if I have properly defined them... why aren't they in these games? Ha ha ha...
What I wanted to mention was how I hoped they might be implemented. I can't remember how it worked in Fallout: NV, but I think you could select 2 advantageous perks, and then select from handful of mixed perks (which had bonuses and then downsides). From a pure character creation standpoint, I'd really like to see no limitations on how many of these you could select, granted that they weren't contradictory. Now, for many that might seem game breaking, and it might be depending on what they are, but if they are done right, I think we should have a lot of freedom to acquire however many we want. I view a system like this as a way of adding personal touches to our characters that can be definitive of our past, our experiences, or our gifts. Putting a limit on that makes it friendlier game-wise, but it seems restrictive in how we build our character. I attribute this to the bad ass factor. Balance is important yes, but I typically roleplay a larger than life character. He is wiser than others, more moral than others, more skilled than others, etc. A super-mer if you will. I would imagine that my character would have a disproportionate amount of good advantages, by nature of being who he is. Now, I don't know what those are, but depending upon the options available I would like to be able to select all that I believe would reasonably apply to my character (again, assuming they aren't contradictory bonuses or traits).
I know it isn't going to be done like that, but I don't see why it can't or shouldn't be. If the advantages aren't egregious then they should be able to play nicely together. I mean, in a system like this, I don't think you are typically limited on the amount of bad traits you can acquire, so I feel as though it shouldn't be prohibited to acquire as many good traits as we want. Ultimately, this would be a test of self control, which isn't a problem I have. If a bonus doesn't fit my character, I wouldn't select it. I am not interested in making a jack of all trades superhero, but I do think that if there are multiple bonuses that apply to my character, then I should be able to select them. I'm starting to just repeat myself, so I'll end it at that, but I'd be interested in feedback!