All subsidies should require reasons attached within the bill itself for the subsidies and for anything that those reasons would suggest should also be subsidized sound reasons for why those other things were not included. It should stipulate that if it is proven in a court that the reasons do not hold up to evidence then the subsidies in question should be rescinded.
This would prevent abuse of the system by special interests. It would make policy-making more logical. The government could not get away with funding corn for ethanol but ignoring more efficient sources of ethanol such as switchgrass. In fact the entirety of farm subsidies would have to be overhauled.
There should be no room for illogical in politics and policy-making. All policy should be tied to clear stated objectives and if it is proven that the policies are not supporting the objectives or that there are alternative policies that would do it better and no sound reasons why those alternative policies should not be pursued then a court should be able to strike down the policy and enforce logic in policy-making.