there are two ways to look at it.
1) The best athlete on the stage should win the weight class, every time. Period. This means the best athletes will make it to the professional ranks, and the IFBB shows will be the best possible shows.
2) The athlete who is most marketable - meaning, short term profits for supplement companies with a consumer-friendly big smile to sell - should win the show. This means the supplement industry - which is absolutely the lifeblood of the bodybuilding industry - will be the strongest (sell the most product to most people) and will grow the most - which will grow the sport the most.
It's a tough call. Look at Chris Cook. Many thought he received a gift when he beat wilmore and haley (two guys who eventually became better pros that chris was). Of course, his smile as the new nationals champ on the cover may have sold more issues than the grille of a less marketable (albeit better physiqued) bodybuilder. In this case, the sales won out, but the sport lost out, as someone not destined to be a pro became a pro, then washed out.
I think they keep a safe balance there - they award the best guys most of the time, but they do need a fresh mainstream smile every 12-18 months, and you see the guy a mile away and know that if he comes in decent shape, he's 1) a pro and 2) gonna be on a cover shortly.