Exchange Server 2013 reached RTM a couple of months ago and has since reached General Availability (GA).
In my personal opinion, Exchange 2013 RTM is not ready for prime time. Microsoft made a decision to release all of Wave 15 (Office desktop applications and servers) at the same time; as well as release Windows 8, Windows RT, and Windows Server 2012 at the same time. I think this decision was seriously flawed. It is obvious that the products were not complete at RTM (witness Windows 2012 and Windows 8 having 300 MB of patches between RTM and GA, and Exchange 2013 not supporting any interop with prior versions of Exchange at either RTM or GA). It is easy to conclude that the RTM dates were artificially imposed.
I have prepared a class on Exchange 2013 for one of my clients and part of that class was to discuss the limitations associated with Exchange 2013 RTM when compared to Exchange 2010 SP2. Note that the rest of the class discussed many of the new features and capabilities that have been added to Exchange 2013. So... the story is not all bad.
But as a summary of my opinion, Exchange 2013 RTM is not ready for prime time. Right now, it can only be installed in a green-field environment (that is, an environment where Exchange did not previously exist), so it is a safe bet that the Exchange team agrees with that as well. We can hope that some updates will quickly come out to address some of the current deficiencies.
This list is by no means exhaustive. And, as always, whether a particular issue is important to your organization requires you to evaluate your environment.
Help -> About is gone
It's very slow.
No S/MIME support
No Public Folder support, either for legacy public folders or modern public folders.
No distribution list moderation
No way to move the reading pane
Built-in spell-check is gone. IE 10 provides spell-check natively, but earlier versions of IE do not. A third-party add-in or an alternate browser is required.
Other things are gone; don't waste too much time looking for them.
No BES support
...on a related note (and likely the primary reason BES is not yet available), the CDO/MAPI download is not yet available for Exchange 2013.
Outlook 2003 is no longer supported.
Direct MAPI access to the Exchange server is no longer supported. RPC/HTTP (Outlook Anywhere) is required.
Outlook now reports that the server is it connected to is <<guid>>@<<active-directory-domain>>. This is intentional, if misguided.
Installation and Architecture
Cannot uninstall individual roles from a server, must uninstall all of Exchange
Install is painfully slow
The Hub Transport role is gone. There is now a Front End Transport service on CAS servers and Mailbox Transport services on Mailbox servers.
The Unified Messaging role is gone. There is a now a Unified Messaging Call Router service on CAS servers and a Unified Messaging service on Mailbox servers.
The CAS consists of three pieces: CAFE' (Client Access Front End), which proxies all end-user protocols to the appropriate mailbox server (completing the decoupling of the MAPI endpoint started in Exchange 2010) and handles Outlook Web App; FET (Front End Transport) which proxies SMTP protocols to the mailbox server and is responsible for TLS setup; and Unified Messaging Call Router.
After an installation or an upgrade, services not starting is an endemic problem. You will likely need to increase ServicesPipeTimeout on your Exchange servers.
Documentation is minimal at best
Deployment and sizing guidance is non-existent.
Cannot be installed along with Exchange 2007 or Exchange 2010
Exchange 2013 Edge server is not available
Forefront Protection for Exchange is gone
For both Exchange 2010 and Exchange 2013, applying updates can often screw up the winrm configuration. If you get errors in EMS or EAC regarding "The WS-Management service cannot process the request", try this first:
Since you cannot interop with legacy public folders in RTM, if you need an Organizational Forms Library, you must create it yourself. To create an Organizational Forms Library:
1. Create "Organizational Forms Library" folder under the Eforms Registry:
New-publicfolder "Organizational Forms Library" -path "\non_ipm_subtree\Eforms Registry"
2. Set the locale ID for the Org Forms Library:
Set-PublicFolder "\non_ipm_subtree\Eforms Registry\Organizational Forms Library" -EformsLocaleID EN-US
It is no longer necessary to set the PR_URL_NAME property.
The Exchange Management Console is gone as is the Exchange Control Panel. They are mainly replaced by the Exchange Administration Center (EAC); which is completely web based.
If you are attempting to use EAC with IE 10, you need KB2761465 (released on December 11, 2012).
The Exchange Best Practices analyzer is no more.
The Exchange Mail Flow Troubleshooter is no more.
The Exchange Performance Troubleshooter is no more.
The Exchange Routing Log Viewer is no more.
The EAC does not provide a preview (or an after-view for that matter) of the PowerShell it executed.
Antispam and antimalware is crippled compared to earlier releases
The E15 AV does not offer a quarantine
The E15 AS does offer a quarantine (for the administrator, not per-user)
Antispam cannot be managed from the Exchange Administration Center; it must be managed using PowerShell in the Exchange Management Shell
Kerberos Constrained Delegation (KCD) is not supported for OWA
This isn't new, but should be reinforced: DO NOT TURN OFF IPV6. Microsoft does not perform any testing to determine the effects of disabling IPv6. Therefore, Microsoft recommends that you leave IPv6 enabled, even if you do not have an IPv6-enabled network, either native or tunneled. See http://technet.microsoft.com/en-us/network/cc987595.aspx
System Center Data Protection Manager (DPM) version required for backups of Exchange 2013 is SC DPM 2012 SP1
Mailboxes and Databases
Mailbox sizes MAY appear to increase substantially when moving a mailbox to an Exchange 2013 mailbox server. In Exchange 2010 and before, only select properties of a particular mailbox item were assigned as part of the mailboxes diskspace allocation, causing under-reporting. Now, all item properties for a particular mailbox item are assigned to the mailboxes disk space allocation. However, some items in Exchange 2013 are now compressed which were not before. This can lead to a reduction in reported and allocated diskspace. So, prediction is basically impossible. Just be aware that it may happen.
Corrupt PropertyTags during a mailbox move are common. Using (Get-MoveRequestStatistics -IncludeReport <<alias-name>>).Report.Failures you can find the rule or message that is causing the problem and remove it.
Changes made to improve Office 365 and hybrid deployments had an unintended consequence (this is my conclusion). When you are performing impersonation (e.g., to open a different user's mailbox via EWS), you should always impersonate using the email address.
As a corollary, it is recommended that the account UPN match the primary email address.
In a change that you won't know about until you need to know it - MRS Proxy is not enabled by default in Exchange 2013. Use Set-WebServicesVirtualDirectory to enable it.
Clean-MailboxDatabase is gone
Update-StoreMailboxState is designed to replace it
Requires that you know the guid of the deleted mailbox
No on-premises cmdlets allow you to find those out!
Get-LogonStatistics is non-operational. The cmdlet is still present, but it doesn't work.
Exchange 2013 Enterprise Edition supports only 50 mailbox databases instead of the 100 supported in Exchange 2010
MRM 1.0 (Messaging Record Management - Managed Folders) is non-operational on Exchange 2013 mailbox servers. The cmdlets are still present, and will affect down-level servers (which you can't use right now), but they don't work with Exchange 2013 servers.
Moving mailboxes using the migration wizard in EAC can generate large amounts of log files for the database which hosts the arbitration mailbox. Use New-MoveRequest instead.
In a positive change, Office Filter Packs are no longer required. There is a new search technology used in all Wave 15 (Office 2013) products and it knows how to search all the Office file formats. This also includes the PDF format, so a separate iFilter installation for PDF is no longer required.
When using Database Availability Groups (DAGs) on Windows Server 2012, you must manually create the Cluster Network Object (CNO) and provision the CNO by assigning permissions to it.
While Windows Server 2012 provides support for large sectors (4 KB), Exchange 2013 does not support large sectors. Emulation of large sectors (512 E) is supported provided that all database copies are on 512 E.
The above statement is, in general, true. Additional capabilities of Windows Server 2012 are not supported by Exchange Server 2013. This specifically includes but is not limited to Hyper-V Replica.
[Edit at 19:55 on 6-January-2013 to clarify why you may need an organizational forms library and to add the note regarding lack of spell-check in OWA (hat-tips to Ben Winzenz and Tim Robichaux).]
[Edit at 21:24 on 8-January-2013 to fix several grammar and spelling errors. Oops.]