I might actually take the sunny devil's advocate view here: the Phillies are the losingest team in baseball history (or something like that - first team to lose 10,000 right?), but if you were born in the '60s (as I was) or even as late as 1979 they've won two championships, played in four World Series and won 11 division titles (eight if you're in the younger group). Is that actually bad?
Yeah, there are a small handful of franchises that, through either money, great management, or both, have been more consistent, and several with more championships, but there are even more with worse results, and almost none that don't go through cycles of boom/bust.
That's not to say the Phillies have ever been good at development, which was frequently combined with being cheap. But they've also never actually done a rebuild before. It's not like the late Thomas/Wade years were on purpose! It's just frustrating that, so far, the results of this rebuild are no different than the results of the team that signed Greg Jefferies or Kevin Millwood (though those teams were decent). In terms of restocking the farm, both in its initial trades and its initial drafts, it has very clearly already failed.