Salient point. It's no secret the Duncan spends the majority of his time at the 5 spot in a small-ball lineup. Meanwhile the rest of the time, Pop throws out guys like Oberto, Thomas and Horry to play center. THe problem is each has his own limitations and is usually overmatched against bigger more skilled players because of their own limitations. (If I see Oberto tap out another offensive rebound instead of grabbing it, I'm going to eat through my own skin.)
Like you, I have long believed the Spurs coaches have relied waaaay too much on Duncan to be the hub of the offense and anchor the defense. It is a lot of responsibility and obviously he's been great at it. In fact, Duncan's true greatness has been demonstrated in the years since David Robinson retired. It's amazing that he's been able to handle all these responsibilities, at an all-star-caliber-level, without the benefit solid frontline running mate in the post-Robinson-era.
As you've correctly pointed out, the Spurs do have deficiencies on their frontline that are being exposed by the Fakers. Fortunately those will be addressed this offseason with the additions of Tiago Splitter and Ian Mahinmi. Personally, I'd also like to see them add a guy like Desgana Diop (Nets).