Super-majority requirements are often dangerous but it is entirely to use them to prevent inclusions of provisions into federal law that only benefit individual states, districts, or companies.
The Fiscal Cliff bill included a rider that explicitly exempted an AmGen drug from Medicare price negotiations and most Senators were not even aware of this inclusion until hours before the vote. Cases such as this are now legislatively routine.
Obviously, being aware of exactly what is in a bill is not enough to constrain legislative quid pro quo and line-item veto power is just as limited by Executive-Legislative relationships. We will only reform our legislative process if we make it much harder to include favors than to take them out.
Let national interests trump special interests.