MM was my first Zelda game of the series, and I was only 10 when I first started this game.
I didn't eve have a n64 at the time, I leeched off my cousin's n64 to play this game.
MM is definitely the most overlooked game within the series. The pacing of the game is heavily on exploration. Compared to OoT where you are constantly told where to go next, MM allows the player to explore freely, but limits the freedom with the three day limit. The game also allows the player to experience the world from a view different from other Zelda games, the players are allowed to explore the world as different races. There are also a lot of side quests that builds of the characters within the game, which is a huge improvement from the boring characters that appear from Oot. In OoT, most characters you can interact with are very much like the ones you find in standard J-RPG; most of them just give hints to what to do next, and the characters are extremely lifeless. MM didn't have as many characters, but the game has a back story for all the minor and supporting characters. The stories aren't generic and boring, but each of them are fairly unique and shows real character traits and flaws.
In my opinion, the game mechanics that makes MM makes it different from any other Zelda title is the complex level design. No other Zelda title has such complex, out of box puzzles. Future Zelda games, such as WW and TP follows the footsteps of OoT, and the puzzles within these future titles lack the complexity. These title focus more on the combat, and puzzles are usually oversimplified or rehashes of older Zelda titles.
The only fault that I can about this game is the length. The length of this game averages about 10 hours without finishing the side quests, and around 15 hours with. When compared to other 3D Zelda, this is extremely short and lack the epic feeling that's usually found within Zelda titles. However, it's hard to fault the game because it only spend 2 years in development, when Oot had 6 years and TP had 4.
In my opinion, MM is the best Zelda in the series. Sadly, due to the poor sale compare to OoT, new Zelda follows the format of OoT rather than MM. There should be a golden rule for Zelda fans to play MM rather than OoT, then maybe Nintendo would consider making Zelda more in MM's format again.