The real reason for the aggregate limit is probably pretty simple. It helps the incumbents who wrote the law. Think about it for a minute.
As of September 25, 2013, the Cook Political Report rated 84 House and Senate races as competitive. This means a citizen, who, for example, wants to help every Republican or Democrat in a competitive race with a maximum contribution, cannot. That contributor would only be able to support nine candidates to the legal maximum, or barely 10% of the competitive races, if he or she donates in both the primary and general election campaigns. As such, challengers feel the pinch of the aggregate cap more than incumbents. Another major source of challenger funding are the party committees, and as already noted, the aggregate caps hurt the parties.