I also mentioned sponges, which are all but removed since they don't push back water anymore and never made it into survival.
True but the only reason sponges were added was to allow for the quick cleanup of water back in Classic mode when water was buggy. It was a temporary hack that was never intended to stick around in that regard, according to the wiki and the sources it cites: http://www.minecraftwiki.net/wiki/
I see no reason for them to remove anything that has a use in the game, even if it is a bad use currently. I would rather it be given a new, cool use.
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The problem with rotten flesh is that it's contradictory. For some reason, Mojang didn't put Villager Meat in the game. Their reasons: it's gross, it's cannibalistic, and it encourages players to kill villagers, which isn't the kind of game this is.
But then there's zombie meat: it's gross, it's cannibalistic, and it encourages players to kill a human-based mob.
It's like no no no, you can't eat a villager only after you've killed them. First they have to be turned into a zombie and partially rotted away, and then it's fine to eat them.
Pick one, Mojang. Either include villager meat, or take out zombie meat. I'd vote for taking out zombie meat, because it really doesn't add much to the game.
Actually, an alternative idea: since rotten flesh is already in the game, maybe keep it in. But make it a rare drop. Instead of it being human flesh, maybe it's the remains of whatever meat that the zombie was carrying. After all, they carry shovels and iron ingots and potatoes. Just make rotten meat one of those things.
Quite frankly, I think it should be tannable into leather, via a furnace maybe. Leather is so hard to come by in the early game that making a suit of leather armour is completely useless because the effort spent farming cows can be easily spent mining for iron.
Of course, that would require balancing the book recipe a little, but big deal. Make each book require an ink sac, or something.
I think there should be a hunger potion. brewing would be nether wart -> rotten flesh -> Hunger potionx3
get hunger for a while. Could be used in pvp (making is splashable of course) to make your opponent unable to replenish health until the effect wears off and he/she eats and heals making it easy to get the upper hand.