One nice thing about Givewell is their commitment to transparency. If you think your time is well spent thinking about optimal giving, you can start with what they've written and try to critique it publicly. (Alternatively, first deliberately ignore their recommendations in order to fight priming effects and try to brainstorm your own independent list of effective giving opportunities, then diff it with Givewell's.)
I think in the long run, the ideal model for effective giving research will be something like the ideal model for science research: publish results, critique the results of others, and try to build on our collective understanding. In the same way that all the world's scientific research isn't done by a single organization, I suspect in the long run we will want multiple organizations doing serious thinking about how to give effectively. The big difference with science is that the laws of physics are the same for everyone but not everyone has the same values that motivate their giving. So the ideal output of effective giving research will be something that makes it easy for you to plug your utility function in and learn what organization best achieves your values.
I want to be informed and to act because I have evaluated the evidence, not just go "with the herd." There's a stigma against simply taking the word of an authority, and rightly so; on the net, the world would be better if more people stopped to think for themselves (does anyone disagree?). But it is also the case that there are many fields in which I have to defer to experts because I simply am not equipped to deal with or consider the problems.
I wonder, is it even worth my doing research on charities, when there exist resources like givewell, which will almost certainly be able to do a more thorough and more accurate analysis than I would be able to do? Should I just defer to givewell when giving my effective charity?
I'll note that there is a difference between values and facts: I might decide for myself that I care more about some issues than others, due to variations in my personal moral calculus (for instance, I may value the well being of no-human mammals, relative to human mammals, more than others, and so chose to support animal rights groups, instead of poverty elimination), but might still defer to the experts with regards to how to most efficiently accomplish my stated goals.
Also, do I have good evidence to defer to the expertise of givewell? I like the idea, their analysis seems insightful, and people on this forum often speak highly of them. But these are all relativity superficial and don't seem like sufficient reason to allow them to dictate my giving (that's just lazily, submitting to the slick-looking authority). How do I evaluate the expertise of experts?