That is really how it feels to me; I think the PDAs were great, but they were placed within a hollow shell.
I think the reason it worked so well in System Shock and not within Doom, is that in System Shock (and SS2), the PEOPLE on board became one of your primary goals. In order to do something, you needed to find a certain person, but odds were that that person was already dead. So then you followed a trail of PDAs to trace that person and obtain the information you needed.
In Doom3, there's only a few persons of concern to you, and they all talk to you directly. So all the PDAs have no effect on you, or your progress in the game. They're just there as backfiller, rather than an actual integral part of your game.
For example, in SS, locked doors / closets did not have the PDA with the code lying in the same damn room. (usually on the same level, but there were several times you'd find the code / key several levels away)
In Doom 3, this became really boring. Oh, this door is closed. There's a PDA. Listen to PDA, open the door.
Locked doors were merely put there to FORCE you to interact with the PDAs.
The emails and voice messages were pretty cool, and did provide atmosphere, but they were never made an integral part of the game experience, imo.
I still enjoy Doom 3 though (and the expansion).