Hmmm... I'm not quite sure I understand what exactly your looking for, but I think your looking for is stories with many layers of plots and secondary characters that are main characters in the subplots?
If I'm not wrong I've got a few to suggest...
Kateikyoushi Hitman Reborn!- There are a lot of characters with their own subplots. I'm mainly thinking of the antagonist/protagonist Mukuro who seems to match up to the definition of a deuteragonist character quite well.
Majin Tantei Nougami Neuro- Though I haven't completed it myself it does seem fit into your request. Don't be put off by the artwork though... it's a lot better than you'd suspect and really adds a lot to the manga... not sure if there is romance though, probably more just subtext.
Nabari no Ou- Has many different sub plots. Their are two romantic pairings as well.
S•A- The secondary characters sometimes become the main characters in their subplots, and at times the subplot almost seems to become the plot for a time as well...
Olimpos- I think this one fits quite well... no romance though. (except for maybe in the first chapter...)
Safe Again Today- This story shifts its focus from character to character, so it has quite a few subplots, and though it is sci-fi it doesn't get technical or anything. Doesn't really have romance, its more subtext.
I second
Full Moon o SagashiteI hope I helped!
Last edited by Tatania at 10:27 am, Oct 1 2010