I don't like "gene" very much because I don't like
Jean. So yes, I pronounce them differently.
Imogen is IM-oh-jin, and
Imogene is IM-oh-jeen. Not that I dislike
Imogene really, I just like
Imogen a lot more. I also like that
Ginny is a feasible nickname for it. I do think
Imogene looks more complete when written though.