I am presently using Gephi to represent plant pollinators interactions. This software is good and easy to use. But I am looking for something else for better representation of pollination networks.
It seems to me that the request should be formulated a little more precisely. What kind of data do you want to present - spatial data or quantitative data and what functions did not have gephi that could be useful for you.
Also, maybe you would show your example graph and write what you are missing from it.
A friend recommend to me this package in R "bipartite" and I have come several articles using the package to analyze pollinator network. May be you should explore it.