Does Migration Assistant allow me to pick an choose which apps to migrate or is it "All or None"?
It's not very granular. Scroll down:
https://support.apple.com/en-us/HT204350
I didn't use Migration Assistant. Look at that list, and you'll notice that if you want to be particular, it's not much different than doing it yourself. Any issues you might have with migrating mail, photos, etc., you'll probably have whether you use MA or manually.
I copied my whole user Documents folder over the network (I was a cable short of being able to use target disk mode—I didn't have a FW800 to FW800 cable—so just did a network transfer over Ethernet). I added any applications needed—obviously, this is super easy for anything you have from the App Store, then download the other important ones. If you want to take the opportunity to Clea up Documents, I suggest copying the old Documents folder as "old Documents", into the new Documents folder. Then go in a pull the most useful folder up one level as you go through, trash anything needless, and leave marginal stuff in place to decide on later.
By far the most work was installing audio plug-ins, because I have a lot. I could have copied them over, but chose fresh installs—not important, but I figured it would also help me keep track of related issues one-by-one, such as my user presets and sample libraries required by some. Some plugins will take some work because they require license files. For iLok plug-ins, it's just moving the key over, unless they were previously installed on the computer instead of iLok, but other use their own software license checks. So, migration Assistant doesn't save you anything there, this was going to be time-consuming either way.
Transferring mail is a big deal, and MA won't save you from that if there are problems. This was the biggest headache, the mail needs to be exported as mbox files, it wouldn't upgrade the old 5,1 archives. It would be easy except for glitches—some of the mbox files import fine, others get truncated, the size doesn't seem to have anything to do with it. I had to divide and conquer—if a mail folder wouldn't transfer all files, I'd split it into two (with smart mailboxes, split by date range—that way no actual copying). If a mailbox segment doesn't transfer completely, split that one in half again, etc., until all pieces import with the right number of messages. Once I figured out this workaround, it was pretty easy if not a little tedious, but I think it was only two folders that had issues.
Transfer your other user folders—your photos, music, movies, etc., and you might have things inUsers/Shared as well that you want to keep. For me, there were also a few things under /Library and ~/Library (typically under Application Support), presets for audio plugins in particular.
I don't see that MA would have saved me from this, and would have brought over junk I could leave behind. Also, I'm not sure I would have caught things like partial mailboxes getting migrated, if I weren't doing it manually, a task at a time, and paying attention to the results. Also, realize that if you're using iCloud, that's were a lot of things particular to you are stored, so a lot of the tedious details sync over automatically, making MA less important. Bookmarks, passwords via keychain, user info...this stuff shows up without you doing anything. At one time, I suppose, MA was a bigger deal.
