Pixelmon
The Pokemon mod for Minecraft!
To find out more about this mod you can check out the Pixelmon website!
Pixelmon development is now at an end. However, the site will continue to run.
Submit bugs here on out issue tracker - Click me!
Pokemon is the intellectual property of GameFreak and is trademarked by Nintendo GameFreak and Creatures Inc.

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These are pretty much my concerns, too, but remember that you can reshape Minecraft however you please. Digging channels between oceans shouldn't be a problem.
And yes, a true ship should become a portable base, possibly even with the capacity to hold a bed.
I'm seeing a huge vessel, indestructible to collisions, black Jolly Roger sails, a furnace-powered propeller, a cabin with a bed in it and a treasure chest (though you could also put a music player and program in the Great Sea theme from Wind Waker). Sail from island to island, take what you need, and when you're done, sail off to the next location. Living on the sea would be a whole other way to play.
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There would also be no harm in making pumpkins and melons truly farmable.
Plus, getting an apple in a chest is a total gyp.
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...NO.
Minecraft isn't about specializing. Its entire appeal is being a sandbox game, which basically means that you will never, at any point, go "Well, that's completely impossible", let alone "If only I were Rogue Class".
Classes are something geared towards combat, anyway, which Minecraft isn't about. Minecraft is more about...mining. And crafting. And building giant sprites of your favorite characters.
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Chickens -I even roomed with one on an island in my newest world until its tragic cactus-related death. It was like a sticom. "CHICKEN! What's me boat doin' all the way out there!?"
Sheep -Why would you kill a sheep!?
Pigs -their little staring eyes fill me with remorse when I kill them, but they're just so delicious...
Wolves -Cute, loyal, and dumb as a sack of doorknobs. Make great decoration as you have them sit in your house so they don't get themselves killed.
Cows -Mmmm...burgers...
Squid -Not all that amusing.
Creepers -They keep quiet and aren't worth engaging without at least a stone sword, and they have a strange sense of not meaning any harm to them. Still, that's a nicccce EVERYTHING YOU HAVE...
Endermen -Ahh, they're not so scary. They kind of make things interesting. Useless drop, though, even when its effect is implemented.
Zombies -Almost harmless, but SHUT UP!
Spiders -SERISSSS! SSSSS! *Hop hop hop*
Slimes -will probably move up in rank when I actually encounter one.
SKELETONS -I WILL MURDER YOUR ENTIRE FAMILY, SKELETON! I WILL MURDER THEM, DIG THEM UP, USE THEIR BONES TO SEDUCE DOGS, GET A MOD WHICH LETS ME URINATE, AND THEN URINATE ON YOU!