My first thought was that this can be said about every computer RPG ever and is inevitable, unless there is an unlimited budget and 20 years of development. It's simply not possible to branch the main story too much and too often.
Second thought is that for me there are actually a lot of consequences to your choices, compared to many other big RPGs. Like which factions to side with, to help someone or betray them. Different ways of solving quests, going against party members or not etc. I mean in some cases the consequences are quite strong, especially when accepting deals related to people helping you with the tadpole.
For me personally in the end I also like the choices that do not end up in immediate consequences. It allows me to roleplay and define my character. In the Raphael example I agree that it is a bit too jarring the way it is written, but I do think my dialogue choices there say a lot about my character and how I chose to play him.
