I see what you are saying about stripping the farm system. I wouldn't say the Phillies traded long term prospect value because to date, what they traded has almost no value. The Phillies traded "potential" value for some actual real value. It's likely that some of the prospects they traded will have some major league value, but most prospects that are not elite never become stars.
I disagree that the Phillies have not won anything since they started trading the guys you mentioned. They went to the World Series after trading some of those guys and to the NLCS a year later. If the measure is winning the World Series, then most trades in MLB are useless since most teams aren't world champions.
While some trades like this are bad from the start (trading top prospects for marginal help now), most don't end up hurting the team who trades the prospects. No outcome is guaranteed, but if you have a shot at winning it all, increasing your chances by trading some potential future value can make sense. I would say that the trades for Lee and Halladay, which did not generate championships, were good for the Phillies, and some of the traded prospects were a lot better than the recent ones we've traded. As it turns out, the best players the Phillies traded in those deals were Carlos Carrasco and Travis D'Arnaud, but I'd much rather have the memory of enjoying the non-championship teams of 2009-2011 than having those guys for years later.
I guess we will not agree on this because we have different perspectives.