A very good point. It's true, TW2 has no timed dialogue - as far as i remember (and i completed it about 7 times)... and those options in AP... well in my opinion they almost don't qualfy as "conversation"... they're more like reacting to a situation... and once you figured out, which charakter had to be treated in which way it's almost embarassing shallow.
To be fair that was the point. In Alpha Protocol Thorton is noted as a master manipulater of people who can easily read someone and base his responses around that. So the dialogue options are more choosing how thorton approaches the situation, rather than individual decisions and exploring the lore of the world. In regards to that, the dialogue system fit quite well both mechanically and in lore. The same system would not fit in a Bioware game, not without plenty of tweaking at least.
Bioware has experimented with real time options using interupts in ME3, and while I find them hit or miss they certainly do add a "flow" to the game that isnt there without them. However interupts do have problems that nag at me. For example many times an interupt popped up I had no idea what would happen. Sometimes it was obvious, but other times I had no idea I what my character would be doing.
One interupt shoots the head off of a robot so no big deal. The other options has shephard grab a man, break his neck, then casually shoot down machinery to wipe out a squad of solders. 
It has the problem to me of not giving me time to process my options and since those mass effect interupts were blink and youll miss them moments, the choice isn't "should I push that man off the building" or "should I hug this character" but rather "should i push this button to see the interupt or will I be missing out?"
Interupts had their awesome moments but I feel unsatisfied with them.