I don't think either make a great champion. Things like popularity, match quality, charisma and how a person carries the title means more than any length of title reigns.
For example, I would have to say Shawn Michaels is a greater champ than HHH because of the way he carried himself, his opponents and the company as a whole while having many great matches (2 with bulldog, vader, mankind). If Shawn wasn't there in '96, I really wonder if the WWE would of made it through those rough years (96-97).
Any reign HHH has had in the last 7 years (even though some of them were good reigns) you could of replaced him with alot of other guys and it wouldn't of mattered too much (RVD, Booker T, Michaels, Benoit, Guererro, Taker all could have replaced HHH and the company wouldn't of suffered one bit).