A question I had recently during a talk was this:
"I worked for a long time for large company X, who many people have heard of. However I recently moved to small company y, which no one knows anything about. I'm looking to change positions. Do I include company y at the top of my resume or emphasize the work with company X??
It's an interesting question, and I have a few thoughts.
The first is that you or I can't necessarily build a resume that doesn't upset some recruiter, HR person, or hiring manager. There will always be people that expect a particular resume format and if you don't provide it, they dislike yours. I have seen people that expect a Summary at the top, your Education next, and then a reverse chronology of jobs, with the dates listed first and then the company name, with your title last.
I can't worry about those people, and honestly, if you're hung up on formatting, I may not want to work for you.
The second thing is that I would highlight my experience in a position or a project first, rather than worry about chronology too much. I would set a chronology on my profile (on a web page, CV, LinkedIn, etc.), but use the resume to convince someone that needs a person to do what I want to do, that I am that person.