Well, there's a lot of stuff missing from both games. This doesn't mean I hate either one, they're both amazing games, but there's a lot of stuff that could've made the games better.
Ocarina of Time
Difficulty, plain and simple. OoT was a joke in terms of difficulty if you ask me. The only way to die on an enemy or boss is to actually try to die. Not to mention, not only are fairies the ultimate way to break the game (one bottled fairy revives you if you die, not that you'd even need it, and with full hearts) AND they're a dime a dozen. Also, the puzzles were creative, but surprisingly easy. After all, who can argue that the twisting corridors of the Forest Temple were uncreative? Were they easy? Heck yes.
Also, the story lacked compelling characters. Even the main characters of the game, Zelda, Ganondorf, and Link were uncompelling. Zelda was just a princess that you only saw a few times who, admittedly, disguised herself as Shiek and that was a big shocker, but that's the most compelling they get. Not to mention, Ganondorf was as cliche'd as you can get with villains. He wants to rule the world, but there's no real motive which sucks. At least they changed that in WW and actually did him right, but that's getting off topic. And Link was just Link. The only interesting thing about him was his origins, which admittedly were pretty shocking and cool.
Exploration too. Exploration was missing in OoT and really that's my biggest gripe for the game. Exploration is what Zelda is supposed to be all about, finding secrets and stuff along the way to your main destination. That's one of the funnest things about the original LoZ, finding secrets along the way of your main quest. But no, OoT completely removed the exploration and made the entire overworld a hub, and that's the biggest thing OoT did that I hate.
Majora's Mask
Exploration for the same reasons as in OoT.
Difficulty. MM was a little harder than OoT, but not by much. The dungeons were a little more challenging, but still absolutely pathetic. One exception being the Stone Tower Temple (God that place was tough). The bosses were also a tiny bit tougher, but they were still pathetic. Odalwa was just time consuming, not hard, Goht was time consuming, not hard, Gyorg was just plain pathetic, and Twinmold was just plain time consuming. Even the final boss was a joke (not to say that Ganondorf and Ganon from OoT were jokes either). Majora's Mask was plain easy, just spin attack him as he comes near you, shoot him with a Light Arrow, repeat until the remains masks come off the wall and start attacking you, and then kill those. And Majora's Incarnation... let me just say, I've swatted flies harder to kill than that guy (okay, maybe I was exaggerating a little). But he didn't hit me once, heck I don't even know if he was programmed with any form of attack in that stage. And Majora's Wrath didn't hit me once.
A more in depth main plot. While the main plot of MM is decent, and had a very shocking twist near the end *spoilers* with the Skull Kid being friends of the Giants *spoilers* but they really could've done the main plot better.