I think it would be interesting to give Ganondorf a figurehead/connection in the government. This would allow Ganon to get resources from the government, if he busts out of Termina after being locked away how is going to compete with an advanced army?
This might help him slip under the radar so he can go about collecting the Triforce pieces. An example is Link to the Past where Ganon uses the wizard Aganim (spelling??) to crumble the light world and use it for his good. The connection might be a background character from another zelda (henchman boss ext.) which could help Ganon break into present Hyrule.
e crit
A comment on the items... They are all awesome but shouldn't there be some interim items that aren't as good. Or the enemies could be really hard.

Will there be any magic in the game? What is Project Nayru? What are the governments agents? Will the game only take place in Hyrule?

I would appreciate criticism for my ideas and answers to my questions.

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