In my opinion Qui-gon ought to actually have been involved in the plot. Sifo Dyas' eventual explanation in extraneous material had him a Jedi who had premonitions of a conflict involving the death of many Jedi...I would go even further, having Qui-gon ordering clones knowing it would lead to the dissolving of the Jedi order and thus on the path to bringing balance to the Force. (even his last words betrayed him to be rather obsessed with bringing that balance). It could, MAYBE, be shown that in TPM Darth Maul was sent, in addition to what is already shown in that movie, to silence Qui-gon from potentially prematurely revealing the plans... but that's maybe a tall order.