Hi Sean,
First of all, many, many, many thanks for taking care of this. Although Marcos is developing a new translation tool, I think that fixing and improving Gtranslator is a very good idea. It is a working tool and most of the work is done. Fixing its major bugs, and adding some new features will be really helpful.
I don't know in what kind of interface improvements are you thinking about. Really, I'm not an GUI designer, so my opinion may not be useful, but I do not dislike ther current one. Have you any mockup or idea about it?
About the X-Generator header, it doesn't disturb in the PO file, and the code is pretty simple, so it should not be a problem. This header may help to identify some problems in PO files: i.e. PoEdit sometimes breaks po files format, so having the X-Generator header is useful to (in case of the tool uses it) track which tool/version has broken it. This field is generated/filled automatically, so it's transparent for Gtranslator users.
About the comments in the PO files, I know they exist, but have no idea about how to create edit it (apart from usin a plain text editor).
I'd like to help you identifying major bugs in Gtranslator and/or suggesting new features or improvements so please feel free to write me if you want.