I am coming back to Nexuis after not having played in quite some time. I seem to remember in the version I played before that the configuration options for the server were much more rich before. I remember being able to tweak the weapon damage, refire rates, what the starting weapon was, and so forth, I've looked around in this version, and can't find anywhere for this.

Am I missing a configuration page somewhere?

Well, you can use console commands in all versions. ( http://ouns.wikispaces.com/cmd )

I understand the console offers a lot of choices, but I seem to remember a rich GUI config ability in Nexuiz. Am I remembering wrong, or was this removed? If I am remembering correctly, can someone familiar with this remember what the last version was that had this functionality?

The GUI CVar editor was removed 2.3 -> 2.4 in favour of faster menu load times.

I think these g_balance cvars are what you're looking for.