Somehow, all of the timelines should converge together. You can't really say it's the "final game" when it can only be on one timeline. Be fusing the timelines together, it allows for a definitive ending. The game needs to have a darker atmosphere than Majora's Mask and Twilight Princess, Ganondorf should be defeated once and for all, with a method of ending his reincarnation being presented. He could perhaps return to being Demise, bringing the cycle full-circle. To show his true power and to continue the dark theme, Ganon/Demise should kill Din and take all of her power for herself.
The ending should show a wedding between Link and Zelda, or at least a kiss. Basically, as long as the ending feels like the complete end of the overarching story, then I'll be happy. I love the series, but I do think that eventually the series needs to have an end somewhere down the line.
The Gorons, Ruto, and somehow the Ancient Robots need to make a comeback, and I want to have the Clawshots and the Beetle back. Elements from each game should appear also, to serve as a sort of tribute to every game in the series that matters. The Master Sword is obvious, but I'd like to see the Four Sword in a 3D console game. In addition to Din, Nayru and Farore should appear as well. There absolutely needs to be an Epona, because she is my favorite of Link's methods of transportation.
However, the build up to this game must be big. Other people want the timelines to fuse together (Is anyone else reminded of the DC Comics New 52 reboot?), and that sounds like a pretty big enough plot point to carry an entire game, so the final Zelda game would have to take off from there. Also, since we're dealing with multiple timelines, what happens when there are additional instances of the same characters, such as Link, Zelda, and Ganon?