Mainly the fact that the same individuals who are doing primary research into humans' impact on the climate system are being permitted to lead the assessment of that research.
Suppose a group of scientists introduced a drug they claimed could save many lives: There were side effects, of course, but the scientists claimed the drug's benefits far outweighed its risks.
If the government then asked these same scientists to form an assessment committee to evaluate their claim (and the committee consisted of colleagues of the scientists who made the original claim as well as the drug's developers), an uproar would occur, and there would be protests. It would represent a clear conflict of interest.
Yet this is what has happened with the IPCC process. To date, either few people recognize this conflict, or those that do choose to ignore it because the recommendations of the IPCC fit their policy and political agenda. In either case, scientific rigor has been sacrificed, and poor policy and political decisions will inevitably follow.