Actually, I like having to track down an Owl Statue or play the Song of Time in order to save. It adds an element of strategy and time management to the game.
You mentioned a cartridge so... Yeah, it doesn't surprise me if an N64 game doesn't look good on a HD set. However, I just played my SuperNES a couple of days ago. I used Wide Zoom mode on my TV and it looked great. The N64 however, not the greatest frame rate in the world, so that could be an issue. I have played the GCN OoT and MM ports on my TV. And while it may not be HD quality, or SD quality (because I don't have the SD Cable - although I will get it for the Wii), it still looks better than it did on my own CRT TV. :\
Anyway...
I love OoT deeply because it was my first Zelda game that I beat (I had played LoZ before, and I had LA, but I never beat them before that). However, in several ways I feel that MM was the better game, and had I played that before OoT that may be my favourite game. MM's story was darker, which is always a good thing. It featured the friend element greatly, which has always and still is a huge part of Zelda. The dungeons, I feel, were designed better than in OoT. They felt more like the dungeons of the 2D games. Especially ALttP, lots of multi-level vertical dungeons. Graphically, textures were improved. While most of the music was the same as OoT's, what was new is brilliant. The overworld theme (not the field, but the theme that plays while in Mountain Village, Ikana Canyon, the Suthern Swamp, and Great Bay Coast) is cryptic and plays upon the darker tone of the game. I also just love Majora's theme.
Majora, as a character is great. Because Majora is the enemy, not the Skullkid. The Skullkid is a conflicted character, with a troubled past, longing for friendship. He finds the mask, betrays his friends, and becomes a puppet. I love it.
The game also had lots of secrets that were fun to hunt out. Certain things that happen at certain times of the day and at certain places.
Much fun. It's sadly on of the most udnerrated Zelda games because it brought Tingle to the world.
It's biggest faults as far as I can see are that we have Tatl in stead of Navi. Navi really didn't bother me. I never found her annoying. Tatl, however, is just rude. The game was also too short. Four dungeons? They should've kept working on it and made it a GCN title.