Update 2/7/13: iOS 6.1 is out now, not sure which of the issues below are fixed by it BUT 6.1 has an issue with excessive log generation and meeting request duplicatication. I haven’t seen this firsthand, but I have seen people on the forums having this issue and so have my peers.
Blog post on current iOS 6.1 issue: https://blog.jasonsherry.net/2013/02/10/ios-6-1-causing-very-high-log-generation-on-exchange/

Update 11/1/12: iOS 6.0.1 released http://support.apple.com/kb/DL1606
Not much details out yet, but it does state “Fixes a bug affecting Exchange meetings.” A bit more details on mashable: http://mashable.com/2012/11/01/apple-ios-6-0-1-update/. Per Steve Goodman (http://www.stevieg.org/2012/11/ios-6-0-1-update-available-including-exchange-meetings-bug-fix/) post the Autodiscover issue still exist in 6.0.1.

Update 10/23/12:
Added link to EHLO Blog Post: iOS6 devices erroneously take ownership of meetings

Update 10/22/12:
Microsoft now has updated KBs on some of these issues:
KB256324: Current issues with Microsoft Exchange ActiveSync and third-party devices
KB2768774: Meeting in Attendee’s Calendar Loses Track of the Meeting Organizer. This KB also list several fixes included in iOS6.
See this related 10/23 EHLO Blog Post: iOS6 devices erroneously take ownership of meetings on this issue.

So as of 10/22 there are three publicly known and documented issues with iOS6 and Exchange. I know of several others from the internal and NDA threads I’m on but can’t share them yet. Microsoft and the Exchange community is STRONGLY suggest you contact Apple with any issues you have. Again, these are iOS issues not Microsoft Exchange issues.

Attendee becomes meeting organizer – Added 10/23

From KB2768744:

If an attendee takes action on a meeting item using an Apple iOS 6 device, synchronizing with Microsoft Exchange Server using Exchange ActiveSync (EAS), the meeting organizer may be changed and replaced by the attendee.

Workaround:

• Recommend that users do not take any action on Calendar items, to include Meeting Requests and Responses in the Inbox, using their iOS device.
• Recommend that users not update to iOS 6 at this time.
• Block iOS 6 using the Exchange Server 2010 Allow/Block/Quarantine feature. See the following post on the MS Exchange Team Blog:
  http://blogs.technet.com/b/exchange/archive/2010/11/15/3411539.aspx
• Block iOS devices for earlier versions of Exchange Server using the following documentation:
  http://blogs.technet.com/b/exchange/archive/2008/09/05/3406212.aspx
• Block anyone who has, or is, a delegate from using EAS.
• Recommend a different client, such as Outlook Web Access or a third-party e-mail synchronization solution.
• Recommend the use of POP/IMAP for e-mail synchronization on the device.

11/1: There is a history of this issue going back to iOS 4.3: Exchange/iOS “meeting hijack” history goes back well before iOS 6
10/23 EHLO Blog Post: iOS6 devices erroneously take ownership of meetings

Autodiscover not working:

11/1/12: This is not fixed in 6.0.1
Per several Exchange MVPs it seems that Autodiscover (the feature that will automatically configure you phone to connect to Exchange based on an e-mail address and password) doesn’t work in many cases with Exchange.

This has been verified by multiple people, see Clint Boessen’s blog post here:  http://clintboessen.blogspot.com.au/2012/10/apple-iphone-ios6-and-exchange.html for a bit more details.

One person was able to get it to work, but only if the e-mail addresses entered on the iPhone matched the user’s UPN (User Principal Name aka e-mail like login).

Disappearing meetings

Added 10/23 and confirmed by Microsoft:

For some attendees or organizer:

From KB256224:

Issue 1.7 – Meetings are missing due on some mobile devices, but are present in OWA and Outlook
When you create a recurring Appointment or Meeting, then change a critical property in an occurrence in the series (for example date, time or location), and then change the whole meeting Series again, the item may not be updated on a device.

The change is reflected correctly in Outlook, but meeting organizers or attendees do not see the change reflected on their devices. The result is an apparent “missing appointment” on the device user’s Calendar.

Cause
The devices use the Global Object Identifier (GOID) instead of the ServerID to track changes to the Calendar item for synchronization requests.

When the meeting series is changed, the same GOID is retained on the whole series. When the device receives the Delete request, sent when the series is changed, in a separate sync request from the change to the individual occurrence, it considers the series change as a duplicate and does not process the update.

Solution
Microsoft believes this issue is resolved in iOS 6. For confirmation or further investigation of this issue, contact the device manufacturer.

Disappear for everyone: (Unconfirmed as of 10/23)

Original text from 10/16
Another issue with iOS6 is related to a bug where declining a meeting invite can cause the meeting to be canceled for everyone. See these post for more details
http://www.macrumors.com/2012/10/03/fortune-500-company-urging-employees-not-to-upgrade-to-ios-6-over-exchange-bug/

The issue appears when users decline a meeting invitation from an iOS 6 device. Instead of simply sending a notification to the meeting organizer that the user will not attend, iOS 6 is sending meeting cancellation notices to the entire distribution list, effectively canceling the invitation for all attendees.