Oh Yhoswar Garcia - We probably won't know what was missed in the process, but by the time it came out (right about signing time) all the top players already had agreements so there isn't anywhere else to put the money. While he has struggled and there are some real concerns about his ability to add enough strength, there aren't a lot of better underlying talent guys you are going to find than Yhoswar.
For Ortiz, once he came to the agreement with the Phillies he was essentially locked out of showcases and out of the complex. He functionally had to sit on his ass for 7 months. That said, Ortiz's size has never been the factor in his outcome. It may have caused some positional worries (and now he is in even better shape and a good defender), it is that the last few showcases he was in really made scouts concerned about his ability to hit breaking balls.
The Phillies front office has been really inconsistent in spending over the years. They have never went over the soft cap before MLB put in the hard cap slots. In the wake of Ortiz they pulled back really hard on allocating large sums to single players which limited the type of players they could sign. Then there is development, where they had a run with complex level pitching, but nothing really else, and that has largely extended to the draft side, so we know it is a factor.
There is also the matter of them not being a premier franchise. The Rays have player dev to lean on, the Yankees are the Yankees, same with the Dodgers (who had just had an absolutely horrendous year the year they spent $30M+), and other teams have Latin American stars or stars in general to point at. If you are choosing between two franchises, there are not a lot of Phillies to point at historically to have been a rooting interest.
I do also think Sal keeps his nose cleaner than some (though they clearly agree to early deals and there is a clear package deal around the Luis Encarnacion signing). I think generally Sal is pretty good at running the whole operation (he used to do more scouting, but my sense is that staff has increased), but the Phillies have been complete garbage at developing anyone.
Could they improve, absolutely, but it is also unsurprising to say all of the same issues that plague the rest of the Phillies also plague things here.