For me, one of the best things about Minecraft, Terraria, and the other games like them that have randomized worlds is the pure surprise of what you might find. However, it's always annoying when your favorite biome is smaller than an airplane bathroom. A little personalized tweaking is a welcome change.
And if you want to reenact Water World or recreate Rapture, now is your chance. Beyond terrain generation, you can set sea level and flood the world if you like.