One of the writers of Freely (maybe Tim Minear?) did a blog post many moons ago where he outlined what some unresolved plot threads were and future episodes. You’re right that it was better off being cancelled. Even Nathan Fillion has said that the reason it’s so beloved is That it never had the opportunity to become bad.

Let me give you the example that stood out to me. Remember in the pilot where Inara gets out a syringe when she hears about Reavers being nearby? Everybody assumed she was going to kill herself. Nope. There was going to be an episode where they got boarded by Reavers and Inara was left alone with them. The crew move heaven and Earth to get back on board and when they do they find Inara barely alive, surrounded by hundreds of dead Reavers. The syringe was full of a Companion drug which kills anybody who has sex with you. So Inara killed then all by letting them rape her.

Mal would have been sweet and tender during her recovery, and that is what would have brought them together.

Probably for the best that one never got made.