Last year I made caramel apple cupcakes, which were exceptionally tasty. But I don’t want to repeat myself!
The only other fall flavor I can think of is pumpkin/spice with cream cheese frosting, which also seems played out.
All ideas welcome!
Someone I work with brought in S’more cupcakes last week. They remind some people of summer, but that’s a sign of fall to me.
ETA: Just had another thought…what if you used a squash bread recipe and made muffins? It’s kind of like a cupcake, you’d have to get creative with the frosting.
Maple bacon.
I thought about this one. Originally Maple Walnut, then looked up recipes for candied bacon and thought it might be good chopped up in the batter or sprinkled on buttercream. Thanks!
The local bakery in the town that I grew up in had this amazing maple frosting they used on donuts and other goodies.
Pecan. Maple Pecan would be awesome.
First, let me just say that no one in the history of time has ever said, “Nah, I don’t want that delicious cupcake; I had that flavor last year. It’s so passé.” Okay, well, maybe some hipster somewhere has said it, but no one with any sense. I love pumpkin, and look forward to this time each year, when I can get pumpkin in everything.
But if you’re really set on something new, then I agree with the maple and nut suggestions. Or, you could do a flavor that uses the pumpkin pie spices (cinnamon, ginger, cloves, allspice, nutmeg) without the pumpkin, like chai, gingerbread, rice pudding, etc. All of that says “autumn” to me.
I originally read the title as “autism cupcake flavors.”
I had a carrot cupcake yesterday which was tasty, and it struck me as very ‘autumny’.
I made some cardamom chai cupcakes recently. They went down an absolute storm.
I also thought about maple. Which really doesn’t make any sense - you make maple syrup in the springtime so it’s really a spring flavor.
Dump the cream cheese and do lightly glazed muffins.
Other than pumpkin: Something with cloves, maybe? Something based on red cake or coffee cake? Look up red velvet mayonnaise cake.
Carrot cake with vanilla/cinnamon frosting.
Sweet potato
Pecan
Cranberry
Turkey 
How about my favorite, hazelnuts? Traditionally more of a holiday flavor, but I think it fits well for autumn too.
You’re totally right, it’s definitely more my issue than it is for the cupcake eaters 
I just find it more fun to try out interesting recipes or new flavor combinations.
gingerbread
something filled or topped with lots of nuts
apple cider
Halloween candy themed – candy corn?
pumpkin… did somebody already say pumpkin?