Some people might disagree, but I cannot recommend you worry too much about the reader and what they want in your story. The reader should be challenged, and frankly, if they cannot follow along with your story while others can, they probably shouldn't be reading it in the first place.
As for the amount of questions, it depends on the kind of story you're telling. I've written all kinds of stories: a fast-paced action adventure, a deliberately paced space opera, a political thriller, all filled with social commentary, and one thing they have in common is an underlying mystery involving the relationship between the visible events to the actual events taking place behind the curtain. Most stories will probably have some kind of mystery, and that does not specifically mean there is no plot. If you know how to form a story, then you should know how to marry mystery with your plot.
That said, I don't think you can ever truly have too many questions in your story, so long as you answer them in the process of telling the story AND if the questions play a part in the story, and aren't there just for the sake of being there.