I've avoided upgrading Icedove to version 3 for a while due to trouble with enigmail (see Debian bug #562714). But after this was sorted out I decided to upgrade.
The upgrade brought with it a host of problems, which made the switch pretty annoying.
For starters, during the first run after the upgrade, Icedove transfered all its files to a new ~/.icedove directory. Good thing that I was alert enough to notice this, so I modified the list of directories I cherry pick for backup. But that was my only lucky break.
The new Icedove insists on asking me for a master password whenever it starts. It never used to do this. At first I thought this problem was related to the issue described in this Mozilla KB article, where Thunderbird prompts the user for a master passowrd even if none was set. But I do have a master password set, and it seems that this is simply a new feature. I could of course reset the master password, but then I'd have to retype all my other passwords. Tough choice.
The new Icedove also decided that it should sync all the folders in all of my IMAP accounts. I think I was asked about this during the upgrade, but I don't remember what option I selected at the time. I had to go to File->Offline->Download/Sync Now->Select... and un-mark every folder except Inbox and Sent (which I do want to sync) in each of the 5 IMAP account that I have.
And then there's this new message indexing feature. It's on by default, and it brought my poor headless laptop to its knees. The machine was busy indexing for a very long while, generating huge files on disk, and then re-indexing on every new email message that arrived. The huge index files also slow down the nightly backups and take up a lot of space, since they get modified every time Icedove is launched.
I decided to disable the indexing feature. Go to Edit->Preferences->Advanced->General->Advanced Configuration, de-select "Enable Global Search and Indexer", click the close button and restart Icedove. I'll reconsider it when and if I replace my current box with a faster one.