Because they are the boss! Minecraft Enderdragons are the way to win in Minecraft, making it not endless. Minecraft has been decribed as "Every nerd's dream" on account of it is an endless video game... or at least, it was!
Because Enderdragon eggs are not of any particular value. For instance, they can not be used to craft any special item. Were Enderdragons not to be removed, I would recommend adding some special item that can be made out of Eggs. Perhapse a special kind of ore called "Enderdiamond" that could be used to craft invincibility armor, 1 hit kill swords, everlasting pickaxes, and/or a whole mess of other things.
In fact, disregaurd this entire article and just add Enderdiamond!