I thought Prototype was a fairly mediocre episode, B'Ellana elevated it slightly though as she does with any of the episodes she is featured as the central character.
As for "Alliances", I thought it was good but the ending disappointed me, "we've tried one time to go away from Federation rules so that means we can never and should never try again". Its just a trope that I really hate in fiction where a good idea is never tried out a second time just because the first time wasn't so successful. It seemed like the end of that episode set the tone for the rest of the series "let's not take any more risks!"
Another thing that also bothered me in that episode, albeit small, was that Voyager fired a photon torpedo at the trabe ship from orbit...that shoulda blown the whole village to pieces!