After completion of peer review, the associate editor usually sends his recommendation to the editor-in-chief of a journal. The editor-in-chief is the one to take the final decision. On this forum I frequently read that the editor-in-chief would usually not overrule / outvote his associate editors. Considering this, I would like to know what factors often delay the final decision on a manuscript. I witnessed it many times that the "decision in process" status did not change for weeks. Why is that? Office hours of the editor-in-chief? As for my understanding, many editors-in-chief are full-time professionals hired by the respective journals.
As for my understanding, many editors-in-chief are full-time professionals hired by the respective journals.
This is the key misunderstanding. EiCs are not paid professionals employed by the publisher, but academics employed as such, typically full professors or people in comparable situations.
You become EiC either by being very senior, experienced and well connected and respected within your subdiscipline, or (more rarely) by founding your own journal. In either case, you will have a lot of other responsibilities, from doing your own research and writing your own papers, over teaching and advising students to committee and other assignments. And then it simply often takes a while for you to get around to process reviewer reports, typically in a batch when you have a block of time.
Speaking as an editor for an Elsevier journal, the system says the review of a paper is complete if two reviewers have submitted their comments. However, I may have invited more than two reviewers. In this case, I'll have to wait for the other reviewers to submit their comments before I make a decision. This happens because during the invitation process, I have no idea how many reviewers will say yes. So I tend to invite more than two reviewers. If all of them says yes, then I'll wait for all of them to submit a response. However, if I have two reviews in hand, and one or more reviewers do not reply after their given deadline, then I can ignore them. Until then, I wait.
The most common reason is, as pointed out in the other answers, the editor or handling editor is busy and not available to look at the manuscript.
The next-most common reason is if the reviewers disagree. Some common results here are 1) involve another editor or 2) get another reviewer, both of which obviously add processing time.
A third possibility is that something went wrong with the original set of reviews. For example, maybe they sent the manuscript for revision when they shouldn't have (e.g. a reviewer got back to them saying their late reviewer will be arriving after all), or one of the reviewers they had invited is actually inappropriate (e.g. undisclosed conflict of interest).