It's always funny to hear people say this in regards to HHH. It has been repeated so much that people automatically bank on it like it's gospel. But when you really think about it in terms of the timeline, it's bullshyt.
It's indisputable that Austin and Rock both dominated (switching between 1A and 1B) the entire time they were full time. Austin retired in 03 and Rock left for good (for that time period) in 04. During the HHH's reign of terror in that time frame, he was responsible for headlining some of the shyttiest Raws in history and stunk it up with just about everybody he faced. The only good outcome in all that shyt is the build of Batista. To make matters worse, he wouldn't even mix it up with the top Smackdown guys (including a prime Lesnar and Angle).
As a result they had to build a real top guy that could actually carry the company (as we all know which fell to Cena in 05). So all in all you have maybe a 8-10 month gap where you could even try to call him the top guy and that has hella asterisks by it cause it was trash (universally shyt on), he buried better talent and he didn't work with the top (superior) talent that were outshining him on the blue side.
The better question is if HHH was as great and as dominant as you say, why didn't he naturally fall into the role of the top guy once Austin and Rock left? He wasn't old (and is still in good shape physically in 2017), had decent name recognition and experience working with the true greats, and was stroking the boss's daughter nightly.
He might be just as out of touch as Vince.
