Thrall feature is indeed core gameplay design. A vague one at that though. Because it is one of the game’s cornerstones, this is why it is so crucial to redesign the basics. Players wouldn’t necessarily spot the differences at first glance, but the added benefit would slide in smoothly.
I hope you are incorrect in two ways; that this vague pokémon collector feature is the endgame and that it encompasses around 80 % of gameplay. 
If you are indeed correct… sigh… my sincere condolences.
Thralls still come with recipes, yes. However, they would develop them in time. These recipes would be dictated by thrall’s culture, biome, personality and race, but otherwise given in a random fashion. Gotta catch 'em all.
Since I thought the thrall feature would work like this to begin with, I was disappointed that it worked the way it did. To me it’s designed to bloat gameplay. We are talking about thralls here after all. If I break their sense of will, why would they have any sense of will left to dictate anything. My order is their life and death; I am their morning sun and evening star. To me the design choice was a mistake of stretch in nature; one that wasn’t thoroughly enough thought.
Being generic isn’t always a bad thing. Deep in it lies truth (simplicity in action). However, there is a way to develop this generic nature. For example, I didn’t specify how exactly they would gain levels. We can fill in content for this purpose.
Better to quit due boredom than disappointment.
I love boredom and here’s why. It tells me that devs did something they believed in, even though it is generic. Something that they didn’t stretch. They could have bloated it, but they didn’t want to lie about their simple truth like many other teams nowadays do. Yes, they say they believe in their game, but their actions tell a different story; story that is inevitably reflected from their product. I like teams that provide the truth and nothing, but the truth. Truth is a firm foundation to build upon. From there we can always arc from feature to feature and be happy with the product, unlike those who stretch and bloat their products. The unnecessary disappointment of their lack of devotion can be heard and seen from their face and eyes. I feel empathy for these people and wish they do better next time around.
Teams stretching gameplay nowadays is mostly our fault, as customers. Our vague enough demand is reflected to the companies and they reflect the same mentality back to us.
If this was all there is, then you would be correct, yes. However, this is a question of balance. The follower limitation and IMEI system were put in place to balance it all out, but the cost is too high for immersion. Hence the new pot mechanic, the radial menu / quickbar limitation and the rack block came to be. They serve as a relatively intricate network down the hood, yet fluid and simple on surface.
I don’t know what a captain is, but from the feedback I’ve received, bosses in this game are boringly indifferent. Just mere bullet sponges with low tactical intellect. One more reason to stay in my cozy treehouse and fish.
With no doubt in my mind it would. Since I already had mass-combat in mind, I also came to this notion while designing the concept. Issue is not necessarily the feature were talking about here anymore, but the bosses instead. There’s only so much that a single network of features can solve. In case the bosses are indeed as weak as you lead me to believe, I believe they need to be updated as well. In the meantime, I won’t leave my treehouse.
Don’t be sorry. It’s not your burden to apologise someone else’s choices; only your own, to those related to them. 
Like I said before, mistakes make a deeper hole for us to climb from. I tolerate the current system to a point and then leave it for good coz it doesn’t fit my standards after all. In case it is developed closer to my standard of quality, I may return, but I rarely do so due the level of disappointments given when first met (or due changes made down the line).
I believe that the vision was at least a bit different, but since I don’t know their actual ideas, I cannot tell in an absolute certainty (yet) if they could do this or not. There are implications that let me believe both yes and no, but I’m lazy enough not to make the effort to know since it doesn’t reassure a change would take place here.
Actually… Not a bad idea.
Sidenote: I’m designing a board game so technically I am inevitably forced to compete with some sweet board games out there. If any modding team is interested about my ideas though, I would be glad to help them out.