Just finished Primordia, getting what I would reckon to be the 2nd best ending. Though I actually liked the bittersweet touch a bit more than the happy version I could have had if I had not missed picking up Crispin’s matrix. Overall I quite liked the story, and at least yesterday I found it really hard to quit, which doesn’t happen with lots of games.
Based on the achievements, there were a few things I did not manage to do, but seems like they did not have a big impact on the outcome. To me it looks like the really decisive choices all happen close to the end.
Edit: looks like it’s indeed possible to lock yourself out of an item pretty early on that is required to get the ending I got.