What are those dozens of sidequests you keep mentioning? A couple of rabbits, a couple of force gems... am I missing anything here?
Literally every time I entered a new town, there was someone asking to be ferried somewhere else. Many of these sidequests involved increasingly challenging routes with increasingly difficult obstacles. In addition, there are several minigames (which I would count as sidequests)--the arrow mini-game, the "cave of ordeals" of sorts in Castle Town, the whip minigame, etc. Bringing new items to old locations would almost always yield something new, and the overworld changed as you got more force gems--meaning more locations to explore.
Depending upon your definition, they might not all be sidequests per se, but it certainly offered more than most Zelda games. It did not have as compelling a mechanic as The Minish Cap (kinstones were ingenious), or as open an overworld as The Wind Waker, or as tight a design as Majora's Mask--but it struck the right balance in terms of side-material. Also, unlocking the dungeons often involved very different techniques. They weren't sidequests, but they had the same feel and kept the game from getting monotonous. Also, outside of the rabbits and the force gems (simply citing force gems deceptively hides the implications of the quests--there are a lot of them, and they also affect the environments of the specific towns and overworlds), there were stamps which forced you to explore each "island." There was also treasure hunting; rupees were actually useful in this game, so being on constant lookout for chests and the like was rewarding.
Ehh, I have to disagree with you. I found the game far too easy, I beat it in a week.
The only parts I found challenging was one puzzle in the Tower of Spirits and the game to get to the Dark Link special boss. I'm not saying that I didn't like the game, I loved it as I do all Zelda games, but it was lacking in comparison to other handheld Zelda games.
"Too easy" simply isn't something I'm willing to hold against a game. Nintendo's released quality difficult titles--see any of the recent platformers on the Wii--as well as easy games that still gave you your money's worth simply because of their scope (The Wind Waker). So long as a game is fun and involving, difficulty shouldn't matter.
In defense of Spirit Tracks, however, I would argue that it actually was on the harder side of things, but, outside of the ill-conceived Tower of Spirits, rarely bordered on frustration. The second boss took me a good number of tries to beat, and I still haven't mastered it. Puzzles make full use of the touch screen because they require you to remember information from earlier in the dungeon. And even common enemies pose a consistent threat because of environmental designs that have you navigating tight spaces. All of this require skill on the player's part. I'm not great at video games, but it's possible that, if it gave you very little trouble, you are.
Most reviews I've read mentioned 10 - 20 hours of gameplay, and in my estimation, it will probably take me about 20 just to get the main quest done. That's not a week's worth of work by any account. I've played my file over the course of several months, in relative moderation with short bursts, and like I said, I'm only on the desert dungeon. Again, it's possible you're much more skillful than I am; however, this isn't something to hold against the game, as it's probably the lengthiest of the handheld titles I've played.