I just re-started a game just for the heck of it, took myself from the beginning through the Forest Temple...
Diababa is pitifully easy to kill. Sure, it's the first boss of the game and the first bosses are always a light touch because you aren't so strong yet, but ... too easy, way too easy. In fact, I don't think the real action of the game picks up until after the Forest Temple.
So, I echo the sentiment of "harder bosses."
Yeah, Diababa was embarrassingly easy, really. I actually thought Fyrus was a bit worse, but that's just me. I do agree that the game didn't really pick up any real difficulty until after the Forest Temple, but at the same time, those early portions of the game were in some ways my favorites. The Forest Temple was pretty challenging and interesting for the first dungeon in a Zelda game. Minus Diababa, of course. Besides him, it actually surpassed any other Zelda game when it comes to the first dungeon... for me at least. I've always thought the Forest Temple was incredibly well-designed considering what it is, and because of that I tend to think it's the best dungeon in the game, if not my personal favorite.
But I'm also lobbing a brick at Zeruda for her comment on Wolf Link. Wolf Link is a large part of the reason why I enjoy the game so much. Therefore, I echo the sentiment that there really should have been more "wolf-things" such as more animals to speak with, more puzzles and clues to find involving Hyrule's wildlife.
I don't think Wolf Link should've been removed either. I do tend to have a little more fun playing in human form, but Wolf Link was still a nice addition and I didn't mind one bit switching to him every once and a while.
Alas, I felt they didn't really put enough time or work into the Wolf Link portions of the game (this tends to be the source of most of my issues with the game, actually: not enough time or work). The Twilight areas were pretty interesting, but there were only three and then that feature of the game was removed entirely. Then you had the ability to turn into Wolf Link at will, but all the depth to it seemed to be gone. There were no new additions.
I would have liked it if, as you said, there were more puzzles and elements of the game tied to the wolf mechanics. I also would have liked it if there were some way of gaining new abilities for the wolf. Nothing you got in the entire game, save for Hearth Containers, transferred over to the wolf, and you gained no wolf-unique powers throughout the entire game. I would have liked it much better if they had upgrades for Wolf Link to give you new abilities or traits to use, perhaps sort of in the style of the Hidden Skills... that could work. Making these changes would have added much more depth to Wolf Link, and made him match up a little more with the traditional flow of the game.
More realistic magnatism in the Goron Mines. I *loved* walking around on the walls and cielings with the Iron Boots, but... oh, come on, if that were in any way realistic, Link's hat would fall off or at least flop downward and his shield and sword would get drawn up. You know what might be cool? If he got to keep the wooden sword and was forced to use the wooden sword and shield within certain parts of the temple becuase the magantism is too high for him to keep the more powerful metal stuff out of Hammerspace/his pouch/Midna's storage/wherever the heck he keeps stuff he's not using. Of course, wooden implments bring up the obvious problem of fire/lava, but that could be an added danger - Don't fall into the lava or get your gear near open flame or you'll lose it. Not all rooms in the Goron Mines would be unfriendly to metal, but having a few high-mag rooms and a need for using the wooden gear while walking on the cieling would be interesting.
That's an exceptionally cool and interesting idea. I like it a lot!
It also reminds me of one thing I've been seriously missing as of late: equipment switching, like how it was done in Ocarina of Time. I loved having all kinds of equipment (tunics/armors, swords, shields, boots) that had different traits that you would constantly switch between to adapt to different situations. I would really like to see a return of this, and I think it could have seriously improved Twilight Princess, especially considering the awesomeness of the Zora Armor, and the presence of the Hidden Skills.