Part fo the problem is that there are 2 Braintree extensions, one that is built in and is advanced. Gene writes both but the 2nd has Apple Pay included. The 2nd one is not compatible with 2.3.0 right now. I was able to get Magento 2.2.6 to 2.3.0 upgrade to work after a lot of trial and error. Here is the procedure I followed.
Obviously backup everything first. I did it on a development copy first.
1. Update all extensions
2. run composer remove gene/module-braintree & composer remove paypal/module-braintree
3. composer update
4. composer require magento/module-braintree
5. composer update
6. Install Magento 2.2.7 (cannot go directly to 2.3.0)
7. compile, deploy and clean caches
8. Install Magento 2.3.0 by following these instructions, but DON'T run the composer update command. Make sure you remove the update folder and do that step, even though it says optional. https://devdocs.magento.com/guides/v2.3/comp-mgr/cli/cli-upgrade.html
9. Edit the composer.json file in the root.Remove any 3rd party respositories. Also remove any extensions you don't need. I found Sendgrid and Bronto were not compatible with 2.3 and only had to remove those. You will know if you try run "composer update" if it gives you any errors.
10. Run composer update
11. Once Magento 2.3.0 is installed, I found that it would not run any bin/magento commands. This was fixed by flushing redis. May be different for your server but mine was.
redis-cli -s /var/run/redis-multi-a751baae.redis/redis.sock -n 0 FLUSHDB
12. compile, deploy and clear caches
You should be good to go! I found one other issue with swatches not displaying and followed the instructions here to fix https://github.com/magento/magento2/issues/19688
Good Luck!
