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The Rebel Alliance would defeat the United Federation of Planets in space combat.
The Rebel Alliance is willing to embrace tactics and strategies that the federation is unwilling to.
The Rebel Alliance is willing to employ terrorist tactics and has done so in the past.
The Federation's standard rules of engagement require it to not open fire unless fired upon. The Rebels would therefore be able to fire the first shot and - potentially - to cause significant damage.
The Federation is bound to a much higher degree than the Rebels by rules and regulations, and by the imperative to take the consequences of actions into account. This could be a handicap in combat.
, the Federation's black ops division that remained in secrecy for over 200 years and engaged in morally indefensible actions for the defense of the Federation, would covertly employ all of the same extreme tactics the Rebel Alliance would choose to use.
The Federation has superior tacticians such as Vulcan's. The Alliance relies on luck, hot heads, space jockies and people with the Force. The Alliance could get out-smarted by smart "Spock types"