I'm not too into Zelda but I thought TP had some of the more engaging dungeons. Though the beginning is slow.
I thought the dungeon quality started to dip somewhere in the late second or early third act. Temple of Time stands out to me; I didn't like how they effectively tried to double its length with what amounted to a full retreading while working with something very like an escort mission. An escort mission with a great big honking hammer, sure - and one of the most entertaining boss fights of the set, not because of the mechanics per se (Stallord or Argorok probably get that nod) but simply on account of
I Can't Believe It's Not Gohma Stop, Hammer Time The World's Most Satisfying Belly Boop hilarious goddamn spider-murder. Yet I remember it left me feeling cheated for some reason.
For some reason Snowpeak Ruins, delicious as the setting was, also left me a bit unfulfilled. I remember nothing of the final trek through Hyrule Castle between the opening cutscene and Puppet Zelda, which probably says enough. And the Palace of Twilight was probably the worst of the lot and all the more disappointing for it. City in the Sky was alright though.
That stated, yes, it's got some very good ones. The primary dungeon claim-to-fame for Majora's Mask is, in my opinion, the Stone Tower Temple (which, contrasted with the Temple of Time in TT, is less a retread and more two dungeons with similar layout) - and while that might hold up fairly well, it also has stiff competition from the Forest Temple, Arbiter's Grounds, Lakebed Temple (probably still my favorite water temple), and Goron Mines, all of which tear apart the other three main dungeons in MM.
The thing that really made MM stick with me where TP only half-managed, however, is in the way its story is presented - the setting, the development of nearly every character and NPC, and the general atmosphere, much of which was a departure from every game previous, and even most since. It felt like a living, breathing world in a way I haven't seen Zelda pull off in any other title, and not for lack of trying. There may be some nostalgia goggles, but it set a precedent to me that made TP - with its excellent combat, mostly well-done dungeons, solid story, and Midna - nevertheless feel to me like MM Lite.
Replaying through the first parts of MMHD and TPHD reminded me that this comparison is partly unfair, but I still can't shake the sensation. Thus, my ranking.