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After hours of searching and reading and trying different people's suggestions (and after skipping by this add on at first since my first glance at it looked like it would be too hard to get working) I went for Import/Export Enhanced and now all my messages are finally converted and into my new mail setup! Once it worked it worked great though it took a few tries using different methods to get there. I can see why some people got discouraged and down rated it but I'd read enough of the different problems that have happened to others and those comments helped me to work my way to the right way for me. It might not be an easy ride but if you keep at it and search around (or ask around) you'll most likely get there.
I was exporting from Thunderbird and importing to Apple Mail and found the following method:
Once you've got the add-on installed (and Enabled) you can find the menu option to start it either under the Tools menu or in the popup menu when right clicking on 1 or more mailboxes. For my export/import I finally found that exporting as "Export all messages in the folder --> EML format" was able to produce a file that Mail was able to use to get all the messages in the folder versus some other options that failed to get them all. I did find that if there were mailboxes that were subfolders of other mailboxes and the top level (parent) folder had no messages that that folder nor the contained folder(sw) would be created. I don't recall if I ever got the contained folders exported at the same time as the containing folders since I had no containing folders with messages to find out. In any case, I just went back and imported the folders that didn't get imported and aimed the exported files of messages into the correct parents. Another issue was that each created folder had a subfolder called "Messages" and when I imported the dumped message files (using the Apple Mail format selection for the import) those extra levels of folders were created in my mailbox structure. So I had to drag and drop the complete set of a mailboxes messages from the "Messages" folder into the next folder up and delete the "Messages" folders. All this may sound crude and bothersome but believe me it was a joy to finally see mail moving to the new program! It may be obvious from the above but you can select more that one mailbox at a time to export (at least on the same level since I didn't try multi-level exporting at one time). The process just reminded me of how difficult things can be and I was glad to have a tool that at least did a very reasonable job for what I needed. I suspect much work went into it and the task being undertaken is a pretty messy one if one considers the number of email programs that might need exported and imported from and to. It's also shows that no one seems to put much effort into trying to make the job of exporting data from their system very easy (like finding the CANCEL button on a free trial site) since no one wants to make it easy to abandon their system for another. (I like and liked Thunderbird but after 8 or so years of it it was starting to mess up a little more than it had been in the past for me; and it's (non)integration with OS X was becoming annoyingly rough edged and not totally functional all the time.) The strange thing is that there seems to e almost as little care put into a program's import functionality as in the export which doesn't seem like it would draw in new users as well!?! But I think this add on is a noble and generous effort to create a tool to help us get by the design flaws of the mail transfer process.
If it doesn't work for you and you've actually spent some time trying a few different methods then it's too bad and I understand the griping but I wonder at that point if you can point to something that will work the way you want. I think there are some utilities that one has to pay for that may be easier though often they aren't any easier or don't ever work even after paying. I think my description above is a little disorganized but I hope that some of my hints aim a few people in the right direction. If you find the thing that works for you then write it up here to help others with this ugly task.