Although reusing the same plot/experiences as all the previous Zelda games do is a major flaw; I'd like to see them shake things up...who knows a shakeup could get me intrested in the series.
Eh, it's not the plot, so much as the formula that stays the same, but that formula kicks ass. Also, I played TP early, before all the spoilers, and believed Zant was the final enemy until it was revealed Ganondorf was in the game. Then the game went epic. For as long as that little surprise was fresh in my mind, the game was God tier.
Examples of amazing plot; WW, OoT, MM, TP. These games have amazing stories behind them.
OoT is wonderfully written, and unlike most of the games before, makes you feel like Link really has an effect on the world. The characters really react to you. Each of the sages you meet in the future remembers you from the past, and their dialogue is generally well done and the game itself was incredibly immersive for it's time. It was similar to aLttP formula wise, but stold the story of Ganon's rise to power.
MM is genius, and deviates entirely from the plot form you've mentioned. Link's wandering a forest in search of a lost friend after OoT. [Most believe it's Navi.] And the ocarina of time is stolen from him, and he's turned into a deku scrub. From here, he has to reclaim the ocarina, and save the world in three days, before a demon trapped in a mask brings the moon down and destroys it. This is probably the darkest game in the series.
WW Shows the repurcussions of Zelda sending Link back in time, and erasing him from the adult time-line in OoT. With no Link, when Ganon escapes the seal placed on him, no one can stop him, and the world fall into ruin. At the last possible moment, the Goddesses themselves intervene,flooding the world and sealing Ganon away with their combined power. Link, in this game, is just an island dweller who's barely turned old enough to wear the green clothes that are a symbol of manhood. Then his sister gets kidnapped.
TP I've already explained.