The Federation have something, that Empire never have - scanners, capable of detecting ships at FTL speed. Basically, Federation have interstellar-range radars, which allow them to control movements of all non-cloacked ships on parsecs range. Any possible Alliance attack could not be sudden or unexpected, and it would be impossible for Alliance to retreat safely - Federation starships would follow them everywhere.
Star Trek has sensors capable of pin-pointing an individual or even reading their DNA and genetic makeup, from orbit (essentially how transporters work), register the exact number, and co-ordinate for each. It also allows their weapons to make precision shots and target individual components with no collateral damage. Star Trek's long range sensors scan other sectors up to 20ly away.