I have dealt with Morton's neuroma for quite a few years. Metatarsal pads helped somewhat. I was never able to pin down a contributing factor from shoes--too big, too small, just right, firm midsole, pillowy cushion--you name it, I tried it. The one saving grace is that it always seemed to stay just on the side of tolerable, so I never saw an MD about it. It seemed to come and go somewhat, but never with a pattern I could detect. However, in the same time frame, I've also dealt with PF (initially) and Achilles tendinitis (later on). It wasn't until after I was finally able to get past the Achilles issue that I discovered what the root of the problem was, and interestingly enough, it was the same problem for all three things: chronically tight calves, specifically the Soleus. If I take care of my calves (and the Soleus specifically) and keep my calves loose, none of these three problems ever seem to crop up. That's my experience, anyway. Good luck.
ps--the one person I know who had the surgical procedure done for her neuroma now has hammer toes and is usually injured. So be careful.