So a friend of mine and I have been working on making a Harem manga. From what I've read people tend to lose interest in them quickly, its harder to hold a readers attention than with other popular genres. We're going to devote an entire year to this project and before really getting into it we're trying to get some feed back. Should we continue with a harem series or go with a more popular genre like a Shounen?
"Shounen" is not a genre, it's a demographic. Shounen manga are those that are created to appeal to boys. They can be of almost any genre.
People don't lose interest in harem comics because they're harem comics, but because they're usually not good comics. The correlation with harem is only there because most harem authors embrace things like shallow conflicts and characters and don't care to or want to write something more engaging. If you can write better, you'll have an easier time gaining and keeping readers.
Create what you want to create. Audiences get attached to individual quality works, not genres. It's true that certain genres have an easier time getting readers (usually this is based on fads), but keeping readers is a whole other story, and it's independent of fads and genres.