1) The author claims cost savings by comparing the prices of American SSNs with European SSKs. This is comparing apples to oranges, since the Europeans don't have the same SUBSAFE standards we do, and their combat systems are significantly less complex than ours. For an American-built SSK, since it would be politically- and morally-impossible to build it with reduced SUBSAFE ("Sure, Mrs. Navymom, I'm sure you wouldn't mind sending your son off in a submarine that isn't as safe as it could possibly be"), the cost of such boats would be much higher than the 25% of the purchase price of an SSN the author claims.
2) The author of this piece at least points out that diesel submarines have a hard time getting across large oceans rapidly. Were the U.S. Navy primarily interested in defending our coast, then sure diesel subs would make sense. However, since the U.S. military in the real world is built around keeping threats far from our shores by threatening the homeland of our potential adversaries, money from a shrinking shipbuilding pool that went to diesel submarines would move the U.S. towards a model where we aren't "forward focused" (or "imperialistic", depending on the arguers point of view). Which, I believe, is what they really want. If so, they should at least be honest and come out and say it, so we can have a debate about that.
3) The theory that "it's better to build more of an inferior weapons platform" was pretty much shot to hell in the two recent wars against Iraq. Many progressive "Reformers" (including Sen. Hart aide William Lind, famous for becoming a conspiracy-mongering nutball in recent years) argued during the 80s that we could get more bang for the buck by building more units of obsolete weapons. Consider the tank -- their theory seemed to be that increasing the lethal range of your weapons system such that you could kill at 2000 yards when your enemy could kill at 1500 yards, you'd get a 4:3 kill ratio. In actuality, in both tank and air warfare, recent conflicts have shown that the better American weapons have about a 100:1 kill ratio, or better. I would guess (based on no real data other than participating in exercises against allied diesel boats) that the kill ratio of an SSN vs. SSK conflict would be greater than 10:1, which kind of argues against the theory that SSKs are "cheaper" in a hot war scenario. Sure, diesel submarines could kill surface ships who blunder into their area, but they sure can't run them down very effectively. In modern submarine warfare, speed is life (or death, depending if you're the hunter or the hunted).
The true aim of those who want the U.S. to shift to diesel submarines is to stop, or at least drastically reduce in an era of limited shipbuilding budgets, the production of nuclear submarines. Those who want the U.S. to "dumb down" their weapons systems (as proponents of diesel submarines such as the writer of the Proceedings article want to do) seem mainly interested in making the U.S. less powerful militarily. I'll leave it to the reader to determine what their motive for that may be.
(In discussing this article, there's probably no need to talk about how much water you've actually had under the keel during various missions. You can just laugh inwardly at the numbers the writer provides.)