Boldly_Gone essentially has this one correct.
Outside of a few obvious like wanting to run for an SOE agent there is no such thing as a best system, there is only a best system for you. So here are some tips to help you decide what is best.
No one system will have everything you want or need, so you really need to be looking at an area of space and not just one specific system, and then select which of the systems you want to use for your base of operations.
With the potential for declining missions you do not want to run (faction missions) having more than one agent for the same NPC close by is another factor.
Having agents from the various divisions (security, distribution, R&D etc.) close by is a plus since it gives you more options on what you can do.
How close you are to low sec has advantages / disadvantages depending on what you want from the game and your experiences in it. If you do not want a mission agent to send you to low sec make sure you choose a system at least 4 jumps from low sec.
Mapping sites like DotLan and agent location sites like EvE Agents can help you choose an area to be in.