E12 has great new features - SCR/LCR/CCR are alone worth the price of admission. But I'll chime in here with a few gripes as well. :)
1. As others have mentioned, the SSL certificate "procedure" is torture. I installed a 3rd party certificate in my test environment and when it came time to renew it I put it off for over a month because I remembered how painful it was the first time around and I knew I'd have to spend at least 30 minutes just refreshing myself on the steps. Even though this was only about a month ago if I were to do it again tomorrow I'd spend the same 30 minutes doing another mental reboot.
2. I like PowerShell and learn more about it every day. I think using it as the basis for Exchange management was a great idea, but I feel like I have to drop into it far too often to perform mudane tasks. I don't like being able to set some SCL levels in the GUI, for example, but to set the Store Junk SCL threshold on a mailbox, I have to drop into PowerShell. Why? If 100% of Exchange tasks are available in PowerShell, 99.9% of those tasks should be present in the GUI. The remaining 0.1% should be so esoteric that I only have to do them once in a blue moon.
(Before I go on, a slight diatribe on PowerShell in general. I think the main problem with the adoption of PowerShell, or the resistance to it if you will, is a simple matter of history. As Windows administrators we're all used to doing everything in a GUI. Cisco administrators would say the same thing as they've been configuring their gear via telnet/SSH for years. If someone gave them a GUI it would feel foreign. For most Windows administrators, the opposite is true.)
3. As others have mentioned, the separation of AD and Exchange tasks as well as the removal of the functionality from ADUC makes sense from a delegation of management perspective, but for a good majority of SMBs the AD folks are also the Exchange folks. Actually, I'd like to see MORE integration of MS and 3rd-party utilities into AD; it would be so nice to tell the HelpDesk folks to "go to ADUC, click on <USER> and go to <TAB> for <TASK>" instead of "go to <THIS TOOL>, then click this, etc."
4. Public Folders. These poor things are the "middle child" of Microsoft collaboration tools - better than a file share but not as good as SharePoint. In our organization they're very handy, however. We don't have the internal knowledge or (frankly) the need for a SharePoint installation. Our users have a strong grasp of Outlook so Public Folders come naturally to them. We also use them as group fax inboxes and group "mailboxes." They might not be as sophisticated as SharePoint but I for one will be sorry to see them go. Utill that day comes I hope that they don't become an afterthought in the Exchange management tools.
5. Now that the Exchange and RTC Groups are under the "Unified Communications" umbrella, I fear that the next versions of OCS and Exchange will be merged into one product with several roles as E12 is now. While I like the Exchange-OCS-AD integration, many SMBs will likely not be able to go "full OCS" for several years due to the complexity of OCS deployment. I'd hate to see Exchange become more complex then necessary.
6. Any additional improvements to make clustering failover/failback as painless as possible for DR/BC scenarios are always welcome.
7. Regarding the EHLO Blog, I'd love to see more "internal/how Exchange works under-the-hood" posts. Actually, you folks should write an "Exchange Internals" book - it would look great next to my copies of "Inside SQL Server" and "Windows Internals." Please? :)
A sincere "THANK YOU!" to all the members of the Exchange Team for a great blog and for listening to us customers!