Playing guitar is a highly personal experience. Every player has different needs, and that is why setting up your new guitar becomes a matter of personal taste.
Ultimately what you are trying to achieve is:
1. Good Action (the least possible distance between the string and the frets without buzzing or rattling of the string against the fret).
2. Balanced, even, electrical output on each string in all pickup positions.
3. Smooth, accurate tuning action and the ability to stay in tune after bending a note or using the tremolo.
4. Last, but certainly not least, killer Tone!