If Ganondorf is sealed than this suggests he somehow got unsealed and then resealed by Link, it wouldn't work. With Majora's Mask the mask lost it's power, it can't even be a threat anymore.
Lol, that sounds cheesier, I liked your other explanation of how the events could go down better. The thing is, no matter what I just think any way it could be done I'd personally find it cheesy. I'd rather Navi not be in the game at all, but that's just me.
Personally the whole Navi thing sounds far-fetched to me. I just can't imagine a way Navi can be implemented into the plot without it feeling cheesy or unrealistic.
Ocarina of Time shows Navi leaving, and while it is never explained why she left we get an idea as to why. The quest is over...
Honestly it could be done in a better way without needing to add another branch to the timeline. We know that there is a pretty long gap between MM and TP, a game could easily be made inbetween them featuring the Hero of Time when he is a little older than he was during MM. The question is what...