So I was also experiencing this issue, and after many MANY backups and resets, I believe I have found a workaround doing the following steps:
*Note* Create all the backups using iTunes, NOT iCloud. After you have verified that your iPhone 6/6s no longer has the bug, you can create a new iCloud backup.
1) Create a backup using your old iPhone 5/5s on iTunes, NOT on iCloud
2) Erase your iPhone 6/6s, and set up as a new iPhone
3) Create a NEW backup of this reformatted iPhone 6/6s in iTunes
4) Restore your iPhone 6/6s using your old iPhone 5/5s backup
*Note* This will copy all your old apps and settings over and will carry over the Apple Wallet bug
5) Lastly, do a restore from iTunes with the new iPhone 6/6s backup you also created from iTunes
*Note* this should transfer over the CORRECT Apple Wallet Settings without the bug while keeping your old applications.
If some people could test this and let me know if it works. Feel free to task me any questions. The only drawbacks I have fund are that it will not carry over any text messages, contact favorites, or app folders, BUT it's the only method I have found so far that neutralizes the Apple Wallet bug for those upgrading to an iPhone 6/6s from an iPhone 5/5s until Apple pushes out a new update.