(Here's a pretty good article that came out several years ago on the weird demands set by the old USDA regulations: http://www.motherjones.com/politics/2003/01/unhappy-meals . See in particular the stuff about the surplus buy-up program and about the perverse incentives the system creates for menu planning. Of course it's Mother Jones, so they think the way to fix this is to reform the rules while keeping the corporate subsidy program in place, which is kind of like having government set a fire in your house, and then -- responsible reform! -- run to the kitchen and grab a pot full of water to douse it with, in the hopes that will put it out. But probably it would have a better idea, and certainly less damaging for all concerned, just not to set the fire in the first place.)
I'm sure it is an example of federal overreach but it's hard for me to see how it represents an increase in federal overreach compared to the status quo ante. The contents of meals in the school lunch program have always been closely regulated and mandated by USDA; previously, the main intent of the regulation was to require that meals would include certain portions of each "food group" (with each "group" representing a different agribusiness lobby: dairy farmers, cereal growers, produce growers, and then cattlemen and the meat industry). The ratios were rigged to ensure that dairy and meat got an artificially big cut, because USDA is committed to buying up a certain amount in surplus per year as a price support to agribusiness. Now the administration is pushing to put through a different set of regulations, which alter the mandated ratios, supposedly in the interest of better nutrition. (But then, the old four-food-groups ratios were also supposedly set in the interest of nutrition; it's just that government nutritional guidelines have a curiously strong tendency to reflect whatever the balance of power between the different agribusiness interests happens to be at the moment.)
The results are probably not going to be any better in the end than the results of the old system. But the old system was also a micromanaging government monopoly, so it's hard for me to see how they are worse, either. Really there is no way to solve the problem at all except to get political control out of school lunches entirely. But you can't get that by reverting to the old rules; you can only get it by dropping the USDA surplus buy-up program. There's no right way for the federal government to manage a subsidy.