Cycling shoes, even pricey ones, often come with fairly basic flat insoles. Since your feet are held in a static position, this can cause discomfort over time. It's worth considering an insole upgrade. Some aftermarket insoles will have an adjustable level of arch support, most will be made of more substantial material than the insoles that come with your shoes and often there will be other extra features like a less flat profile and a midfoot bump to help support your feet better. You can also buy bespoke insoles made to match your feet.
There are a number of different shoes on the market such as the Bont Riots and the Lake CX402s that can be customized through heat moulding to fit the shape of your feet. This means that the shoes should perfectly support the arch of your foot, ensuring that you should be very comfortable and power transfer should be improved too as your foot won't move around at all. If you have flat feet or arch-related problems, heat mouldable shoes could be the solution.