How do bakers come up with their recipes? HELP ME?!

like JJ said, most of the time any new recipe comes about it's based on an already formulated recipe. all cakes are based on a basic mathematical formulation of ratios, how much flour to sugar to eggs, etc. and then modified from there. so if you find a basic vanilla cake recipe and a basic chocolate cake recipe just go from there. flavor extracts are a great way to start as well as substitution, if your recipe has water, try coffee or some kind of juice or other liquid, if it calls for vanilla, add orange extract instead. it may not always work but you'll start to be able to tell what you can and can't change in recipes.
another great way is to delve into fillings, even the most basic cupcake can seem much 'fancier' if you add a filling to it and filling can be anything thick enough that the cake won't absorb them (jams, frostings, citrus curds, etc.). and having some unique frosting/cake combinations is also an awesome way to go and you can go about finding new frosting flavors the same way you would cake, find one you like an modify it until something works.

as far as flavors,
basic chocolate and basic vanilla are always a must
red velvet is usually a good one to have as well as a carrot cake
people tend to like things with strawberry so maybe a chocolate or vanilla cake with strawberry filling/frosting
the chocolate and hazelnut combination (Nutella) is big right now and chocolate and peanutbutter is always popular
some kind of cookies and creme, oreo kind of thing usually goes over well
something with mint might be good
maybe a caramel apple cupcake (apple spice cake with caramel filling and brown sugar frosting)
you could make a mock hostess cupcake, chocolate cake filled with whip cream topped with ganache and a white frosting swirl
maybe some kind of lemon or citrusy cake
something based off the flavor of s'mores would probably work out well
banana creme or banana and chocolate is good

basically any sweet flavor combination you can think of can work as a cupcake with a little experimentation and creativity

pastry chef

I went to pastry school at johnson and wales and we mainly used books with formulated recipes, so most chef's use a lot of recipes that they were taught or have read in a book. If you want to make your own flavor then try with a basic vanilla cake recipe and add flavors. I make a amazing french vanilla cake and all i did was take a hazelnut extract and added it to a basic vanilla cake recipe. The only major tip of advice is always measure what you put in your batter! In baking there is no pinch or dash... I would just start experimenting on what flavors you like and go from there. The most important thing is to have fun, even if it takes you 65 times to get it right.. Happy baking!!!!

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look in cook book ;) lol kidding they use thier brain