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The only issue you will have when "running a season" is the fact that the tiers jump around a lot when progressing from the first adventure of the season to the last. In other words, you can't start a 1st level PC in adventure #1 from Season X, and actually be able to progress through them in order.
Instead, if you are planning on running a PFS campaign, you want to put together story arcs that make sense.
This thread gives you lots of options for that:
There are a couple different posts that he did highlighting different story arc options (be it by "season" or by telling an actual story). Plus there is plenty of discussion so you can get ideas.
And, as others have mentioned, lean toward Season 4 and beyond if you will have 6 players.