What does this mean?

Hi Gibbs.  Here is my take on your questions:

1) How can one human be the best of God's creation when there are billions of galaxies who may have civilizations millions of years older than ours who may have attained a type of knowledge greater than what we know on earth?

The key word is "may".  There "may" be civilizations on other planets.  There is no evidence.  So, until we know for sure, this is a hypothetical situation which does not actually refute the idea of Muhammad (pbuh) being God's best creation. 

2) If he was the greatest among all things created by God why die?

Why not?  He was still human.  Furthermore, being God's best creation does not mean that he was entitled to more benefits.  Actually, it carried more responsibility.  He had to earn that title.  And so, he had to do more to please God.  He fasted longer, prayed into the twilight hours of the night and was required to live a simple life, with no major luxuries.  He was God's best creation but he slept on a bed made of palm-fiber.  He was God's best creation but he died without having any wealth to his name, as he was required to give it all to charity. 

3) if he was the greatest among all things in the universe why even to this day his own brethren still fight amongst their selves over the same religion?

Well, that would be the fault of his followers, not him.  Conversely, his followers also started a scientific age which eventually fueled the European Renaissance.  How should we interpret that?     

I think the best of Allah's creation is intelligent beings as such. Human beings capable of understanding his universe and capable of worshiping the creator.
I think prophets are important to remind the rest of humanity about this. Our universe is not just a lifeless boring soup of quarks and electrons. It contains treasures such as planet Earth. The more you think about this, the more remarkable it becomes.