Edit: I will also admit that I kind of suspect that with Reeve it would be more a matter of manipulation, as was suggested, then actual corruption. Rufus plays at being reformed as he takes more and more control, extending his influence, while still playing at being out for "the good of the world," leaving the other characters in conflict about how to deal with this situation and whether Rufus really means what he says as well as forcing Reeve to reevaluate his own thoughts and feelings on the matter.
I like the idea that Reeve gets played by Rufus. A "shadow government" and "take-over of WRO" plot would work well as a major obstacle for our heroes.
I think it should go so far to the point that Rufus takes the leader position of the WRO, after having nestled in his own people in the organization and paying off a great deal of WRO personnel.
When he stands in his new office and everyone has left, I imagine him saying to himself "
The Shinra Company...is reborn."
With some dramatic music to accompany this, a new chapter of the game begins. This story shift makes airships inaccessible to our heroes (who has previously been backed by the WRO), so now for a time you are forced to wander the overworld and find a new means of travel. Basically, many resources will be taken from you and this will affect the gameplay, adding a sense of desperation because the protagonists are already in the middle of preventing a disaster that will be brought upon by Genesis.
About airships, I actually think the game should start out with the heroes having a flying vehicle available. This would add a non-linear element and the option to visit some familiar locations that aren't important to the story mission at hand. Not all towns and continents should be accessible from the start though and some caves/dungeons may be labelled with a "Level Recommendation", so you don't enter when you are too low level. We need these elements to constrict non-linear exploration to some degree, just so the player doesn't spend the first 10 hours visiting every town in the game.
Details that need to be figured is just what Rufus' philosophies and goals as the new head of WRO would be. I think the other people on this board can figure it out better than me.
Something that I'd like to do is for the game to show a "
crack in his shell". Say for example if one of the Turks died, would this make him more desperate and obsessed with gaining power? If FFVII:EC takes place 10 years after the original game, Rufus must have grown more fond of his suited comrades than even he anticipated. We will never "see him bleed or cry", but say for example that as leader of the WRO he pursuits Genesis, the killer of one of the Turks. Rufus loses focus and becomes reckless, making even the surviving Turks question their leader.
Somehow this should be the seed for why Rufus loses (or gives up?) his position as WRO President. But after this is done, how do we end his story arc? Should he help the heroes (like in Advent Children) to help prevent the impending disaster? Should he sacrifice himself for a good cause? Should he die because he is too stubborn?
When Rufus' dream to attain political and financial power gets crushed, what does he have left?
EDIT: Lol, Rufus going after Genesis would be a neat parallel to the original game where he went after Sephiroth. While unoriginal, I like the symmetry of this.