Are those C&C written but just not implemented yet? Sea, were any new choices added with new patches in beta?
I do know many of my suggestions with respect to gameplay tweaks, small dialogue updates and fixes, character stats, difficulty, quest options, etc. were implemented, and I'm sure the same is true of the other suggestions given by whoever else was involved in the pre-beta.
My opinion time: The thing with content generation is that it is a lot slower inside the realm of an organized development studio than "just add some more stuff" would suggest. If bugs can get replicated they can get fixed super fast. Content has all sorts of people involved - programmers, designers, writers and possibly artists too. It also has to be tested, even in a beta environment, to make sure it doesn't break anything. That means C&C tends to take substantially more time than tweaks and fixes do to implement. Remember, it's only been two weeks since they even got any outside feedback from anyone.
Sounds to me like inXile are bad planners.
Significant C&C story/structural stuff is already implemented and was certainly planned months in advance. There is one
major piece of C&C in the beta already, which is on a scale that most games do not do. The issue that exists right now, in my opinion, is that there aren't enough things like follow-up side-quests to decisions are made, or enough bits of flavor dialogue; it's missing a lot of those little things that follow you around as you play.
More of my opinion time: You tend not to notice a lot of that stuff, especially in your own work, until you have the time to sit back and enjoy it as a player would, or get someone else to give hands-on time and start interrogating it. I had the same issue with Thirst despite having a really good sense of the C&C on a larger scale throughout its development; the smaller bits and pieces of reactivity that add up to create real immersion only happened as I played more and more and found myself asking logical questions like "why can't X happen?" or "hey, Y character would be great for this role instead if he/she survived earlier." In other words, I think very little of that can be blamed on a lack of planning, unless you are positing to sit back and have a game 100% finished design-wise before production ever starts - which is not very efficient.