I was thinking, what if Qui-Gon had never brought Anakin back to Coruscant? Or just left him there longer. How would it affect the plot?

Having Qui-Gon leaving the dangerous "chosen one" behind, would secretly make Qui-Gon the true Phantom Menace.

Having only Qui-Gon and Obi-Wan know about the boy, then the death of Qui-Gon, it leaves it up to Obi-Wan to takes things upon himself to go back for him and train the boy. The way it should of been. Obi-Wan should be resposible for the tragedy. This would really help alot of consistency issues throughout the saga, and possiby make some scenes later in ROTS and ANH a little more ironic and emotional.

Im not really sure when to bring Anakin back into the film, but somehow someway make Obi-Wan be the one who is ultimatly responsible for the tragedy of Anakin, not a character that doesnt really need to be in the movie.

If this was ever done correctly, I can see this really helping the plot in TPM.

This is just a basic idea that can really be built on I feel.