The job of the director is to make the viewer truly feel the characters' situation. I believe he did that, and quite masterfully too.
The truth is - space exploration is slow, brain meltingly slow ...there's really not much to do for most of the time. After a while, there's nothing to talk about other than petty operational concerns.
The crew just drudge through their painful existence, monitoring the same old operational concerns for months on end until none of it has meaning. The conversation stops, seconds lengthen into an abyss of solitude and any minutia is seized upon as the brain desperately seeks distraction.
Now, how would YOU film that?
Did the movie make you feel bored? Did you feel it just seemed to drag on and on painfully slowly with little of note happening? Good! You were supposed to!
When he reads the instructions for the toilet... were you just HOPING that this was finally some plot device, something was about to happen? Were you agonised that it was, yet again, nothing significant.
Well, welcome to the crew's life! Any tiny bit of new stimulus, however banal, is explored to its limit as the brain seeks out ways to entertain itself. Even the toilet instructions become worth a second or third read.
Kubrick captured the mood perfectly!
If you think a couple of hours of low-stimulus activity was difficult to sit through, imagine months or even years of it... the slow gnawing boredom and creeping insanity of life in space.
If he'd have made it an action movie, he'd have betrayed his audience...
... you'd have left understanding nothing of his characters' world : )
You can remove these scenes or shrink them and still get the same movie.And you can easily just cut from 'I will take the Ring to Mordor!' to 'I'm glad to be with you, Samwise Gamgee!'. A movie is not just about A and B. It's about getting from A to B, and the ride the audience takes along the way.