Bowden never did. He never made strong moves to shore up the starting rotation, either by trading for pitching prospects or signing good free agents. The only big trade he made, for Denny Neagle, was negated when he turned around and sent him to the Yankees the following year. This could have been a blunder, except that Neagle imploded in the Bronx.
Bowden was great at getting that "extra guy" who could give your pitching staff an edge; but you can't build an entire pitching staff with "extra guys." When you try, you get guys like Rob Bell, Jimmy Haynes, Steve Parris, Ron Villone, and Paul Wilson taking the mound every fifth day.
Not only was pitching a problem, but Bowden's performance in the amateur draft speaks for itself. From 1993-2003, the Reds managed to draft and develop just one successful starting pitcher: Brett Tomko. And by successful, I mean just a few years spent in the majors. Tomko worked out well enough, especially as part of the package that brought Ken Griffey, Jr. to Cincinnati. But when you look at the team's drafts (and you can, thanks to Baseball-Reference.com), it's no wonder Bowden was scrambling to find somebody to take the ball every fifth day. If the best you can do in ten years is Brett Tomko, then you have a serious problem.
Offensively, Bowden can always point to the 1998 draft, when the Reds took Austin Kearns in the first round and Adam Dunn in the second. But the only other good hitters taken during Bowden's tenure were Aaron Boone in 1994 and Joey Votto in 2002.
So what was Bowden's great success in Cincinnati? He was good at a lot of the little things, but the big things seemed to evade him. He was better at forming a bullpen than a starting rotation, and he was better at trading for short-term lineup solutions rather than signing a legitimate building block.
Thus, when Bowden got the job as GM of the Washington Nationals, it was a surprise to many. Here was somebody whose biggest problem was building talent from the bottom-up, and yet that's exactly what he was asked to do with the Washington franchise.
The Montreal franchise came to Washington with the understanding that they had to have a new ballpark; outdated RFK Stadium would only be the temporary home for the Nationals. But the city council balked at the amount of public financing required to build a new stadium. Before any deal was struck, they wanted assurances that the Nationals would commit a significant amount of private money to the project.
This may not sound like a big setback. But Bud Selig wasn't used to this. After the Baltimore Orioles opened Camden Yards in 1992, Selig helped seal the deal for eighteen new ballparks across the nation, almost all of them financed with huge amounts of public money. The MLB not only asked that the taxpayers swallow a chunk of the new ballpark's cost, but also that the team be given numerous tax breaks and incentives. In the past, city leaders had given him all of this this and thanked him for it.