I came across this list of Criticisms of SharePoint 2007. I'm not trying to ruin the party right here before the official launch of SharePoint 2007 but like all technologies, the product does have some shortcomings.
No doubt that SharePoint 2007 is a big step forward from the previous version and unquestionably the product will continue its immense growth rate. However, as it has been the case with WSS 2.0 and SPS 2003, there will be a growing list of annoying things with WSS 3.0 and MOSS 2007 as we're getting further into the nuts and bolts of it. This is to be expected and it isn't a big worry if we can manage it with workarounds and tools or simply understand the limitations of the product.