I've always had the same issue with caged pedals, small platforms with concave shape, large outer area pedals with "thin/spindly" platform part so the gaps between the axle and the cage are larger; pedals where the material around the axle is higher than the cage, all seem to hurt my feet eventually.
Try a set of DMR V12s. These seem to be really comfortable and a best of all worlds if you get the lighter Mag versions.