I would love to see A return of the Crosssbow as a upgrade to the bow.
This.
And I think the cannon would be more likely to replace the bomb arrows, or even the bombs, before it replaced the ball and chain.
As for other items I'd like to see, they mostly involve the Ball and Chain and the Spinner. I loved these items so much, I'd hate to see them go just as quickly as they appeared!
Ball and Chain: This item brought something new to the tables: destruction of property. I had fun breaking tables, flooring, walls, and even suits of armor. This item was well thought out, and brings some uniqueness to the Zelda franchise. It was a very good weapon, too. Swinging it around, you could get oncoming enemies way before they got you, without stopping to aim at each one. It was fun to throw around, acted as a shield of sorts, and was just a good idea in general. It should stay.
Spinner: Another great idea! Perfect to cut across sand, and ride upon railings, right? I liked how it was executed in the game. It was mostly used for transportation, but could also be used as a weapon. It wasn't used enough, and should appear in the next game as well.
Crossbow: A wonderful upgrade to the Bow, without going into guns! Really, PH and ST are moving forward technologically, meaning they should really consider this idea. It would make a lot of sense, especially with the upcoming train.
EDIT:
Triforce of Courage: Okay, so it's technically already in the game, but what does it do for Link, really? Not much, I can tell you that. Ganondorf gets amazing strength from his Triforce of Power, Zelda gets wisdom from her Triforce of Wisdom, but Link only gets "courage"? Well, he's saving Hyrule from Ganondorf, which you would think would be in favor of the Goddesses. So why doesn't Farore, at least, aid Link in his quest? I'm suggesting something like Farore's Wind. But more to it than there was in OoT.
Farore's Wind shouldn't just be used to teleport to dungeons! That makes it practically useless, since you're hardly running in and out of the dungeon anyway. So it should work more like Midna's teleporting system did in TP. This would be much more useful to players, especially if the land is as massive as it was in TP, OoT, etc.
Something else that's been discussed between myself and others is the possibility of Farore's Wind summoning up a tornado to sweep through the room and harm every monster. This would be an effective area of effect attack, thus making it easier to take on hoardes of monsters.
Finally, Farore's Wind should give you the option to change the wind direction. This, of course, would only be useful if you could use it to glide. Well, that leads me into the next item I would like to see.
Farore's Wings (name pending): The name hasn't been decided upon yet, but I figured this would be good. Basically, it's an item that gives Link bird wings that allows him to glide. Also given to Link by Farore, he can now ride the wind. You are able to glide up but lose speed, or down and gain speed, and have a certain amount of boosts available to you. There is a meter that measures how long you can fly (similar to the magic meter), and once it runs out, you float down until you touch the ground. Once you touch the ground, your boost ammunition returns.
This has been discussed by someone else and I, and has gone from armor to wings. I think it's a good idea with a lot of potential, especially when used with Farore's Wind.