it all depends on your strategy at the table, and on your expectations. if you think you are better than the opposition, you want to have more money at the table because that means in your big hands you can win more. it also gives you more leverage when/if you want to bluff (there really are only two reasons to play your cards - either to bluff or to get value). auto rebuy only saves you from needing to click on each table a few times in each orbit...
if you are severely outclassed on the other hand, you may prefer playing shorter, because a shorter stack negates the skill advantage of the other players. then again, why would you be playing in that game, especially online?