It seems to me the game is designed to be experienced more than once, and that it is purposefully made so that different styles of play- patient players who go slow, people in a big hurry who just want the highlights, that sort of thing, have entirely different experiences.
In the same way that taking less direct paths results in whole different experiences, I suspect that Larian is well aware that some companions can be "missed" on the first playthough, and that this is a feature, rather than a detriment.
In any game that really features "choice" and "different paths", this is a desirable result. It's a credit to the designers that there are so many possible things to experience, in so very many ways. I know I've found totally unexplored areas, events, and characters on each of my 5 playthroughs. Each time I really thought I had covered most everything, but there are lots of areas that are quite out of the way and unexpected.
To me, this is all a plus.
