Should the "earmark" process be reformed or possibly banned?

Note: My question was inspired by a side conversation generated on this thread.

As some of you may know, all appropriations legislation, that is, any legislation having to do with money, originates in the House of Representatives. In 2013 the US Speaker of the House of Representatives, John Boehner announced a renewal of the ban on “earmarks” for the current session. What this means is that members of the House of Representatives can no longer insert itemized requests into legislation. Great, right? it means no more wasteful Bridges to Nowhere! But wait! According to an article in the New York Times, this ability has been replaced by the practice of sourcing requests to full committees or appealing directly to agencies to have part of the pie shipped their way.

This is a way to do an end-run around the ban, and seems to be more shady, and provide a more elusive money trail.