The choice of problem relates to the choice of genre, if the writer is working in genre fiction, and the choice of primary plot problem determines the primary reader expectation. Mystery readers expect a murder (or at least a serious crime), and expect the protagonist to solve the crime. Spy-thriller readers expect a conflict of spy v. spy, agency v. agency, with a specific goal that is met on one side and frustrated on the other. Hard-SF readers expect a problem directly involved with some aspect of science (and some of them demand that it be physics, math, or engineering); they expect the protagonist to solve the scientific problem. Romance readers expect a relationship problem, and expect the protagonist to end up with a (at least temporarily) successful romantic relationship. Stories that satisfy reader expectation without boring readers (in other words, offer readers something new, but not something that violates the prime plot directives) are successful in the marketplace. Writers need to be aware of readers' expectations for the primary plot in each type of book, and write in those areas where fulfilling that requirement isn't a hindrance and doesn't make the writer feel trapped. If you don't want to make solving the crime your primary plotline, don't write mysteries. If you don't want to make relationship development your primary plotline, don't write romances.
In short forms, the main plot-critical problem needs to be introduced early and kept in the forefront: a short-short has no space for adding plot complexity by adding problems. Piling up problems in a short short ensures that most of them will be left unresolved, with a good chance of annoying readers. With each increment in length, the writer has a choice: another problem can add complexity to the plot and may increase the punch of the story's climax. Or, it can dilute it. That will depend on how the writer handles the relative importance of the plotlines that grow from each problem.
Consider a typical long-mystery plotline: the detective character needs to find out whodunnit. The detective character also has a relationship problem at work, and a relationship problem in his/her private life. The detective's motivations for attempting to solve the three (at least) problems arise from different parts of his/her self, and create three different plotlines. From the reader end, the reader bought the book knowing it was a mystery, so a successful "whodunnit" plot must ensue, or the reader won't be satisfied. So if the writer emphasizes the private relationship plot, and skimps on the "whodunnit" plot, the existence of the other problem dilutes the overall success. Ideally, all three plotlines resolve close to the end of the book, in a way that satisfies the requirements of Plot, or--if this is a mystery series--one or both subplotlines offers enough in the way of plot structure to convince readers that a good resolution will come along in another volume. "Rolling" subplots in a mystery series can be an effective way to retain readers' interest--it's not just another whodunnit, next time, but a chance to find out if the detective got married, if he/she got a promotion, if his/her parent/spouse/lover died, etc. (Used to great effect in Alexander McCall Smith's series about Mma Ramotswe and her "No. 1 Ladies Detective Agency.")
Each plotline can draw problems from more than one layer, even in stories with multiple plotlines. As long as the reader finds it easy to stay oriented in person, place, time, and causation, these additional complications merely enrich the story. Multi-layer problems for one plotline give the ability to shift from one to another to maintain tension/suspense (the essense of reader "glue") without the obvious sinus-wavetension/relaxation rhythm of a single-level plot. Just as we must cope daily with challenges on multiple levels, requiring us to prioritize responses, characters with multi-level problems offer the same opportunities to writers. As long as the writer avoids too obvious a sequence (physical/emotional/mental/physical/emot
But for reader satisfaction, for readers to stay oriented, one plotline must be strongest, must be the thread readers return to when you've taken them on a subplot side trip for awhile. The primary character attached to that plotline should be your protagonist, and your protagonist should be the most developed (in terms of levels of motivation) in the story. The difference in importance need not be great...but it needs to be in your mind even when you're writing in a secondary character's viewpoint.
Some writers are outline plotters and some are instinctive plotters, but both have to be aware of the necessities of Plot and of balance between the main plotline and the subplots. Modulating that balance with the choice of problems (specifically the number and "size" of the problems) offers writers a natural way to maintain the impulsion of the overall plot structure.