(First time poster, LONG time lurker)
My daughter is 14 and started Epiduo back on Sept. 7. She had been on Benzamycin for about a year and it stopped working, just like your son's experience. She was switched to Duac in early summer by her pediatrician but didn't have a lot of success with it. I also asked her ped about an oral antibiotic to get a "jump start" of sorts to help clear her up, but she wanted to wait and see if the Duac could work on its own, which is understandable.
Her dermatologist switched her to Epiduo and decided to put her on doxycycline also and her skin looks 100% better compared to how it looked this summer. Is it the Epiduo or the doxycycline? Well it's both. I do know that my daughter has had absolutely no side effects with both treatments, but I'm also having her eat yogurt or drink drinks with probiotics in them daily. She will eventually be tapering off doxycycline in a few months and then we'll see how it goes. She has had none of the Epiduo side effects with redness or dryness. I think she has tough skin, lol.
If your son does get put on Epiduo, go out to their website and get their coupon, which means you don't have to pay more than $20 per month. Saved us a lot of money.
Acne treatment is so much trial and error - good luck to your son and hope it works out.