Right now, I think there's only one change I'd make to the Gemini spec: formalize the use (or at least acknowledgement by clients) of ANSI escape sequences that control color and bold/italic. I'd make inline links a compatible extension (the use case for this is Wikipedia).
Discussion
For inline links: you'd suffix the linked text with [1] or something, and after it, use a link line where the "name" is "[1] linked text: blablabla" or "[1] linked text" (without quotes). This is very similar to how existing HTTP gateways operate.
Should it be specified that clients should ask users if they want to turn it on for a site before rendering them, by default? That might help discourage sites from using it where it's not needed or where it might be misleading.