How "unnatural" is the universe? Looking to read up on the impact the discovery of Higgs boson has on the String Theory I came upon these two paragraphs in an article about the Higgs boson Nobel Prize:

One possibility has been brought up that even physicists don’t like to
  think about. Maybe the universe is even stranger than they think.
  Like, so strange that even post-Standard Model models can’t account
  for it. Some physicists are starting to question whether or not our
  universe is natural. This cuts to the heart of why our reality has the
  features that it does: that is, full of quarks and electricity and a
  particular speed of light.
This problem, the naturalness or unnaturalness of our universe, can be
  likened to a weird thought experiment. Suppose you walk into a room
  and find a pencil balanced perfectly vertical on its sharp tip. That
  would be a fairly unnatural state for the pencil to be in because any
  small deviation would have caused it to fall down. This is how
  physicists have found the universe: a bunch of rather well-tuned
  fundamental constants have been discovered that produce the reality
  that we see.

I thought this was a gross exaggeration of how weird and unnatural the universe is (it was after all written by someone who starts his sentences with "Like") so I wanted to get other opinions on whether the state of our universe is really as weird as "finding a pencil balanced perfectly vertical on its sharp tip"?
 A: The article you quoted is really badly written. Instead of unnatural the correct world should have been "tuned" or something similar. The issue is related to the fact that we know that, if the fundamental constants of nature would have been slightly different, the universe would have been completely different. For instance, carbon would not be formed at stars. So many scientists think that our universe is finely tuned to allow humans (or at least carbon based life) to exist. There are many theories about why nature seems to be this way. The one I find most plausible is the "anthropic principle", which in this context states that if the universe had been different, we would not be here to ask that question. Many physicists dislike the anthropic principle, but if you believe in the multiverse hypothesis, in which there is a huge (perhaps infinite) number of universes each of which has different values for the fundamental constants, or even the physical laws themselves, a universe would "look like" fine tuned to allow self aware beings, but that is an observational bias because only those universes whose laws allow self aware beings will contain self aware beings capable of asking that question.
A: The example of unnaturalness you describe is the example of the mexican hat for the higgs mechanism ( if you look at this page up on the left you will see the mexican hat in the PHYSICS logo).
As all should know this symmetry is naturally broken at our energy levels, as in this the example, which  is correct, that the pencil sits precariously and can break its symmetry at a small environmental impulse. It is natural that the pencil will fall, as it is also natural that if you let down a huge number of pencils there is a probability that one of them will balance for a tiny amount of time on its nose. So the "unnaturalness" claim about nature is remarking on the small probability of the pencil balancing for a while on its nose.
Theorists and cosmologists in particular use the naturalness criterion , i.e. how probable a hypothesis is, to search for theoretical models that will describe the beginning of our universe with the Big Bang where the energies are such that in their theories it is natural that the symmetry is unbroken. (It is a stretch of the pencil analogy to say that energy could be naturally supplied to keep it on its nose , holding it for example :) .
In conclusion, the state of the universe we find our selves in is not like the pencil,  metastable states end up at the ground level very fast at the level of energies the universe has now. Everything is very naturally in its ground state. It is the models proposed for the  evolution from the singularity of the Big Bang  that introduce the metastable concept in such a graphic manner, but again in the models the concept is natural for the level of energy that would allow the metastable states.
Now if the pencil is a stretched analogy for the results coming from  attemtps at a theory  of everything models which have many vacua, and some may be lower than the vacuum we are in at present,
a)there is no established theory of everything now, just proposals on which the naturalness criterion is always imposed
b) again we are talking probabilities, and if the probability to tunnel to another vacuum is larger than the age of the universe the problem of metastability becomes irrelevant.
