You are completely correct. One way of thinking of it is how the league assigns value to picks. High first rounder is more than half a team's entire draft budget. Even at our draft slot, our first rounder was half the total budget. A team which fails with it's first and second round draft picks and primo $ international signees with the frequency of the Phillies really can't overcome that problem and find success. FAs are too expensive to fill a draft void, even for a high budget team.
I don't blame the Phillies at all for pitchers who flame out due to injury, as Gowdy did, although I strongly suspect he was injured when we drafted him. We've done relatively well both internationally and 1st/second rounders on pitchers. I think pitchers are where your medical and training staff can provide a big advantage by reducing the number of guys lost to injury. Also might have saved many promising OF's we lost to repeated leg injuries.
I think the Phillies have had a systemic problem with their amateur scouting organization. As Austinfan said, they have found some good guys later in draft. That is individual scouts, such as our Long Island scout who gets thrown later round bones by the execs every year and freqauently gives us very tasty bones. When you fail in the first two rounds, that says to me that the scouting director/national cross checkers/gm/ all of our assistant geriatric advisors who have their thumbs in the first and second round pies are severely failing us. As we learn more about the Eagles draft dysfunction as Howie lets the owner largely choose first rounders far too frequently, I feel reinforced in this opinion. It is possible to have good scouts and draft badly if the guys higher up the food chain don't trust the area scouts enough and have poor judgment, as our higher ups have seemed to have post-Arbuckle. This has been more than a decade-long problem, with Nola the notable exception.
As you say, we used to draft extremely well in the period which led up to the 2008 championship. Middleton really needs to get good people to do an in-depth analyhsis of how our organization went from so good to awful.