The best solution is to get some younger feet.
Our feet have a thicker fat pad when we are young that really helps prevent foot soreness from things like cycling for hours on end, even when using wood soles with cork insoles like we all used to do.
If you can't do that, then I guess you'll have to come up with some sort of plan B. In my case (size 15 with long, wide toes and non-existent heels), plan B consisted of using a Spenco insole with some additional foam underneath the balls of the feet. This added foam is placed under the insole and is fatter in the middle than on the outside edges. I think Specialized does a higher-tech version of this shape with their insoles. It seems to encourage cycles of flex/relax that keep the feet from swelling.
Also, check the camber of your cleats to make sure you aren't tipping out to the side and be sure to not over-tighten the front straps. Check the strap tension after you have warmed up. You may be surprised by how much your feet have swollen up.