I always thought the DS was a bit too primitive when it was new. the 3DS is a much greater enhancement over old tech. I personally feel that the ds Zelda games should have been on the 3DS.
Anyway, Spirit Tracks; i like it a lot better than PH, the main temple is much better, the travelling system feels more in tune with the control system, actions like rolling have been made easier and the presentation is a lot better than PH.
Also, any game to make train gods seem believable or at least not stupid and tacky, is definitely doing something right. Characters like Chancellor Cole and Staven/Bryne are somewhat fresh archetypes for a Zelda game and they definitely intrigue. there is an interesting political air that the game playfully toys with and the representation of Princess Zelda herself is perhaps the best written of the character that the series has to offer.
New Hyrule may be relegated to sight-seeing along straight lines but the world around you that you see from your train looks as every bit thought out as games like OoT and MM did. New Hyrule feels like a huge place with mountain ranges, expansive fields and coast lines (a particular gem within these elemental realms is the Ocean Realm) even though you can't move around on foot in it. the idea that you can always see the Tower of Spirits in the background where ever you are gives a good air of geographical placement of yourself within the world and makes the whole experience feel more immersive.
Boss battles are just as fun as they were in PH and some of the dungeons are, in my eyes, the best i've seen in a 2D Zelda, particularly the early ice dungeon.
As a side note the items are handled quite well and unlike most games since ALttP, Link will use a lot of his items in more than one place.
The sidequests in this game are also enjoyable, it is fun to search out those rabbits.
However, while i do believe that Spirit Tracks is a very good game and perhaps one of the most overlooked and best 2D games since ALttP, it does have some problems that i really wish it didnt.
The Spirit Flute is a pain, i can spend ten minutes trying to get a song down with a sage and feel lucky when i pull it off rather than happy that i did it.
Slashing with the sword still feels clumsy especially when you're predicated with being on the move.
The story itself, while intriguing for a Zelda game, is very much non-existent through most of the game, we get a few major scenes in the beginning before the first realm and dungeon is visited, then we have little to no exposition at all until a brief scene more than half way through the game and then the story fizzles out again until the end of the game. Much like Ocarina of Time did but in ST it is very noticeable, you do end up wondering to yourself what are the enemies doing with so much free time when they have evil deeds to be getting on with.
But Zelda will never win any award for narrative structure or story pacing so we can let that go.
All in all ST is a very pleasing game. We could have done without Ph and gone straight into this and the Adult Timeline would have been all the stronger for it.