[spoiler
There are consequences for using the two major tadpoles.
The one that evolves you to half illithid is more of a cosmetic change but an unmistakable warning that you need to stop. And the major tadpole...trust me, you don't want none of what that has to offer...it changes the ending for your character in a massive way...you are doomed to become a normal mind flayer under the control of an elder brain, your companions all leave you, even your love interest, and if that wasn't enough your soul is destroyed...when you die you will be ended forever. It's not even worth letting Karlach use it because while it saves her life in the short term she will be gone forever when she dies...better to let her die now and maintain her eternal soul intact. It's the worst consequence and punishment possible.
I think the main issue is that there's nothing really connecting these choices. They're completely divorced from everything you did up to that point. Using either of the two "major tadpoles" isn't really contingent on using the tadpoles in the past, nor is it contingent on your relationship with the Emperor (or any other character for that matter). When people talk about meaningful choices in CRPGs they tend to expect some level of interconnectivity. They want their decisions to have cascading effects on the world and see that reflected in later choices. If you can pick every evil choice in the game, kill every person you meet and still get the generic good ending then that's sort of bullshit. Likewise, giving into temptation every single time by using the illithid and inserting every tadpole you get into your eye socket only to have the same outcome as someone who never even looked at them just because you rejected the "ultimate tadpole" is an exceedingly hollow choice.
Yes. It certainly feels like two different games, you have the first part, with tons of reactivity, racial and class specific dialogue options, different choices that affect the story and how it carries forward, a character that gives you an item intended to be an important story artifact (Omeluum's ring), and then everything that occurs outside of specific Tieflings that may show up later, are never revisited. The game proceeds and you enter Act 2, there is still some racial/class dialogue options, but the story is much more railroaded, which is bizarre given that we were told Act 2 is the longest, which it is certainly not. Almost all of the side quests still plug into the story of the Act itself, companion stories, and the main story itself to a degree, then you get to Act 3, all the side quests have absolutely nothing to do with the main plot, except for
it could be argued that none of the companion stories really have much relevance either given they are not resolved by the end. The main story feels very thinly threaded and weak, with the two main obstacles being a joke and having very little relevance. Their entire motivations are
"join us, betray the other
then you get railroaded again into the final sequence, which feels like a slapdash last minute addition and is sort of outside of the main flow of the entire story leading up to this point.
Two different games, and I'm pretty sure it feels this way due to significant re-writes all the way up to the final months of release. They should have stuck with a story, framed it correctly, and had it flow consistently, instead it's a patchwork of plots that eventually split and feel completely irrelevant by the end, and finally we are then presented with an ending that is not an ending, which just caps the entire experience off by saying "none of your decisions mattered, and none of the companion specific quests really mattered (or, in the most generous fashion, mattered very little). The entirety of any decision making throughout the entire adventure culminates in the final minute and none of your decisions leading up to that moment have any relevance as to whether or not those circumstances would change or be permitted.
It's a very confusing situation to be in, the beginning is so good, and then latter half is such a mess, what cognitive dissonance...