One Pay Commission for every deapartment was of the past economy, now India is growing a superpower. Traditional one Pay Commissions is a reflection of poor economy.
If at all a traditional pay commission needed it should be for the employees of the Administrative Services only.
Other services such as Defense, Scientists, Railways, Postal, Armed Forces, Teachers, etc should not be included in the administrative. They should be independent separate of their own.
Otherwise no one Pay Commission can match the charasmatic.
Employees should be hired to serve in a department only after known the pay scale differences and agreed with.