I personally would've voted for the phantom, but not for chasing players who haven't slept in 5 days; I would've voted for them for being able to go through blocks, and being a flying mob, and if they spawned regularly like other common nighttime mobs, this would make hobbit holes and dirt/sand pillars impossible; they've always been the easy way out of danger, and I personally feel that's game-breaking. The phantom would've solved both of these problems, and forced players to actually build a shelter instead of just getting out of it super-easily.
As for their current behavior - Minecraft (at least before 1.7) generally focused on mining and caving, but you could do whatever you wanted in the game as you pleased. The current behavior of the phantom further drags it away from free-form play - as Creeper mentioned - by forcing you to sleep at the worst times - and can easily be ignored in the game anyway; with its not being able to go through blocks, your simple wood box shelter would still protect you from them at night, and of course they would despawn at day (I could be wrong though). Also, you'd think the phantom would go through walls anyway since it's technically a ghost.
But all that shows that they've really just fallen away from survival mode in recent years, and why people would vote for such a mob - it just shows that people would just vote for what looks best, especially if everyone else voted for it.
You've mentioned that Minecraft focused on doing whatever you wanted, and yet you mention that players should be building an actual shelter instead of a hobbit hole.
Being able to get away from monsters with just a quick fix like that can defeat the purpose of ever building a shelter, and while admittedly I do like the hobbit hole idea, it's effectively game-breaking in that sense. In fact, if you wanted a hobbit hole that protected you, you would need to find or craft coarse dirt, which would protect you from the phantom but is not available everywhere.
But if it goes through blocks, how is building a shelter any better than digging a shelter? Also, it's a sandbox game. Who cares whether your shelter is made out of dirt or Nether quartz in the first place?