I think the main problem is that by "intuitive", a lot of people mean "sloppily glossing over distinctions as if they don't matter". Sometimes people try to simplify problems by treating new or difficult ideas or operations as if they're like other more common things, but this leads to problems insofar as those things actually differ. Intuition is hugely important and valuable in problem solving, but your intuition doesn't tell you the truth if you've trained it by thinking of things as being something other than what they are.
High level constructs should map in as straightforward way as possible to the more complex, low level details they represent. For example, if something is a pipeline, and a user finds pipelines conceptually difficult, trying to make the interface hide the fact that its a pipeline doesn't actually make it less difficult. The thing is still a pipeline, and can't be dealt with correctly any other way, so hiding that fact makes the problem even more difficult by making it less clear.
But if you've been thinking about it in the right way, then your intuition points you at creative and effective ideas about how to use it, without having to first reason through the details. Its as if you have a correct model of the thing somewhere in your mind that you can feel, even when you don't trouble yourself with the details, so what you feel about it tends to be right. In general, in my experience, most things that seem 'counter-intuitive' usually seem that way because they weren't explained and understood in an accurate way, not because they would seem counter-intuitive otherwise.