As has been the case over the last year there have been some very strange decisions on E12 which are still in existence from the above list.
1) Public Folder Tree Management - you are removing a very userful tool that was perfected in EX2003sp2. You are essentially forcing companies to retain Ex2003 servers to managed that function. whilst the aim is to remove need for public folders I work with companies that have on average 3-4Gb Hierarchies (the biggest being 7) and this will not be popular as a full move to sharepoint isn't going to be a quick affair.
2) Snap-ins for DSA.msc - you could essentially get lynched for this or it opens the door for third party vendors products such as Active Roles to support PSH in their GUI - but thats not a product for all companies.
3) Failure of PSH to support the AD schema 100%- whilst this is not listed the PSH doesn't reference attribute properties in the AD schema and will causes issues with custom applications on invalid recipients in some instances.
4) The reliance of PSH scripting is going to prove challenging to update existing scripts mostly on the grounds that attributes in AD have a different name through PSH. There was supposed to be a attribute mapping document provided but this hasn't seen the light of day yet.
The logic behind the back bone technology of 2007 is great and will be popular but a few of the decisions above i perceive have been taken from a technology point of view and not from operations management. bottomline is there is going to be a heavy reliance on third party vendors or Scripters to make administrative tools to support not only for the small shops but for SI's who have a 'C' team admin model.