I think one thing to keep in mind is whether or not people who donate money through a system such as Watsi, would have otherwise donated that money to some other type of organization, and whether by donating through a Watsi like system they will be more likely to donate to other types organizations in the future. These questions could definitely use some study (I'll bet there are some already out there).
Anecdotally, I'm not someone who normally gives to charity, but I gave through Watsi, because I could see and to some degree feel the real impact of the money. As a secondary effect, I actually feel more charitable, whether that means I will give to other types of organizations remains to be seen, but I would not discount the halo effect systems like Watsi may have.
People who are already giving the max to GiveWell-supported charities should not divert their funds to Watsi.
People who have more to give and want maximum impact should follow GiveWell's recommendations.
However, many people have not given to the max, nor do they care so much about maximum impact. For them, there is Watsi to direct their dollars to a noble cause, rather than on Minecraft-themed plush toys or something.
Anecdotally, I'm not someone who normally gives to charity, but I gave through Watsi, because I could see and to some degree feel the real impact of the money. As a secondary effect, I actually feel more charitable, whether that means I will give to other types of organizations remains to be seen, but I would not discount the halo effect systems like Watsi may have.