In most RPGs the choice how to solve moral dilemmas is left to the player, with the player having to deal with the consequences of that choice. For example, Baldur's Gate which you defined as quote: "choose the best answer metagame", allows you to actually make choices and then hits you hard with consequences of your choices, since the rest of the party that does not agree with the choices you make will protest and argue with you, they will leave your party and sometimes will even attack you or start fighting among themselves. What they will not do is throw a dice to settle an argument. Divinity lets you make a choice and then if the other player is not happy with that choice, resolves the matter with a dice roll. After that you are left with playing along with the decision you have not made and with no effective way to somehow go against that particular route.
Most cRPGs provide no fucking consequences whatsoever outside of the outcome to the quest itself. Consequences within your party due to conflicting good-vs-evil binary morality are an exception (which games, aside from some IE games did that, anyway?).
In the case of D:OS it would anyway only make sense to implement something like that with the companions (i.e. Jahan and Madora and hopefully any others that will be introduced eventually in patches). The two main characters are clearly intended by Larian to stay together - the whole design (from mechanics to backstory) is build around two main characters.
One might not like that, but it's the way it is - and therefore whatever you do, keeping both main chars in the party is, at least currently, mandatory.
If you chose to give them an AI personality - that means that they might make decisions you don't like. As Ulminati said, there's a workaround for those decisions you absolutely can't live without when insisting on using the personalities. Nevertheless, this is a cRPG and as such has the limits of all cRPGs. You have pre-fabricated consequences build around some design principles (like the two-character thing) so every outcome will be limited by that.
Personally I find the AI personalities to be an interesting approach to cRPGs, even if that sometimes means that I don't get the intended outcome.
The decision-making mechanics are typical RPG mechanics, however. Your characters have conflicting opinions and want to convince the other that they are right. What do you do in an RPG? You chose an abstract mechanic taking into account your skill at arguing, the situation and some influence of chance. In other words, you do a dice roll. What's so confusing and/or unusual about that?
Now in D:OS you have the somewhat strange RPS mini-game on top of it. Space-bar should bypass it in favour of a roll, but as of now that option is bugged and seems to produce a 50:50 chance all the time. Guess that will be fixed in one of the next patches, though.
If I remember correctly, when I play with AI completely off I get to choose the answer for both characters. Playing with only one character having AI on, and letting him start the dialogues I have not tried, but from what you are saying (if I understood it right), this would only allow me to choose the answer myself for both characters. However, that just equals to turning the AI off, and as I have explained before it is not really a fix.
Not quite. It means that you make the decisions for whatever char is active and initiating dialogue.
In case both have an AI personality, the one which is controlled by you is using your input, the other one is using the personality you gave him.
So if one AI personality is choosing an answer you don't like, you can bypass it for this conversation/decision (with the caveat that the other char might still make a bad decision due to his AI, but you can e.g. set your "main" char to loyal AI).