In his presentation to the Norwegian Academy of Science and Letters, Hans von Storch outlines a number of issues with the IPCC and suggests possible solutions. I thought these were pretty interesting, particularly the bit where he discusses dealing with dissent - I've added emphasis to the "ouch" bit.
1. Dominant (“best”) authors are no longer responsible for describing consensus (as “lead authors”) – (otherwise they assess their own work).
2. Political and economic interests are not informing the process of assessing the legitimate scientific knowledge.
3. An independent “ombudsman” - system takes care of complaints about factual errors (in determining consensus and conflicts of interest). – possibly fulfilled.
4. Assessment by IPCC is independent of acting persons. Dominant authors must be frequently replaced.
5. IPCC is providing an assessment of the contested issues. In particular it describes dis-sensus. IPCC encourages falsification.
6. Political and scientific functions within IPCC must be strictly separated.
I think HvS has probably identified the main issues but I'm not sure about the solutions. For example, no independent ombudsman is ever going to remain independent in such a politicised field. The IPCC is meant to be independent already, but clearly it isn't.
The problems of politicised science are impossible to avoid when science is run and funded by politicians but while this remains the case, there are still things that can be done to make the IPCC process more trustworthy. This is why I am surprised that HvS doesn't mention transparency at all. It is fair to say that nobody is going to trust the output of the IPCC any longer unless all its deliberations are public. The output of the reports cannot be decided in advance by a handful of influential authors - witness Overpeck, Mitchell et al in the Climategate emails discussing how to deal with sceptic arguments ahead of AR4. Everything to do with the reports - and I mean everything - needs to take place in public.
This is not to say that there aren't good things in HvS's list. Rotating authors out seems a reasonable step, although I'd go futher and have people from outside the field doing the writing. Anyone within the speciality has a vested interest in the status quo and for such important policy decisions this is unacceptable. Far better to have a neutral do the writing, taking evidence from experts as necessary.