Wouldn’t it have been interesting if Qui-Gon was revealed to be Anakin’s father in Episode 1 at the end of the movie like this?

It might even be possible with the footage available. Just cut the conversation about Anakin’s parentage with Shmi, Qui-Gon’s bewilderment about the boy, the midichlorian test. Make it so that going to Tatooine is purely Qui-Gon’s idea, and edit the dinner scene to include a meaningful glance or two between Qui-Gon and Shmi.

This would also work going forward. Anakin’s love for Padme is a mirror of his father’s secret relationship with Shmi, as well as his dream of freeing the slaves. That he can suddenly become a Force ghost at the end of ROTJ is similarly explained since his father also discovered the ability on his own and presumably after his death.