The problem with having qui-gon being the creator of the clone army, is that he believes that Anakin is the answer to all the galaxies problems (the problems being personified in the sith).

It could however be a cool revelation that the the clone army was designed for anakin to lead perhaps? (which does actually happen)

The PT though needs an obvious villain, who openly opposes the protagonists, the republic and the audience. Having Dooku mentioned and referred to in TPM, visually revealed in AOTC and defeated in ROTS could provide that surely?