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.
Section 31, 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"