Hi..I know this thread is a bit old but just thought that I'd share my story.
I was first prescribed Epiduo a few years ago, around 2010-11. I was about 12, but I had quite bad acne, even some cysts. (Previously I'd used Differin, which worked for a while, but it wasn't effective enough). After I began Epiduo my skin cleared a lot, and for a while it was mostly clear. My prescription ran out around mid-2012, and I just recently started treatment again.
Something I noticed is that for the first week your skin clears a little, then during the second-mid-third week, your skin may become flaky in the areas around your mouth, cheeks, and (ugh this is so annoying it happens a lot) underneath your eyes. The areas are light red, tight, sore, and occasionally a little itchy. Putting on moisturisers will usually sting your skin a lot, so if this happens what I recommend is papaw ointment used topically before you go to bed. Also, make sure you tone down the amount you're using, just apply it topically, at least until the irritation goes away.
After another week-two weeks your skin should have stopped flaking and be clearer than before. To prevent the flakiness happening in the future, be sure to not use too much cream, and don't dry out your skin in other ways (e.g. not using moisturiser in harsh environments, exfoliating too often or too vigorously lol, putting your face in an oven...I don't know just pretty obvious stuff really)
Epiduo is by far the most effective acne treatment I have ever used. If you've got the peeling skin problem, I recommend sticking with it for a little longer 'cause it may work out in the end!