Well E2 to me was nothing more than a distraction from the main plot and a shameless rip off of DS9's children of time.
Countdown was a fun episode, but come on... we knew from day one Major Redshir-- I mean Hayes, was gonna die at some point.
The whole Degra arc really is symbolic of the greater story arc that's drug along all season. Archer tries deceiving and manipulating him, it doesn't work, so he tries diplomacy and it does work. Really the biggest weakness of the whole arc is Dolim. Sure we need a bad guy, but bad guys have motivations usually beyond just being evil. Dolim sure is turning a blind eye to overwhelming evidence just to satisfy his need to be evil.