Yeah that seems to be the biggest problem so far, with or without Enemy Within. The problem is that the campaign isn't time-restricted like, say, FTL, which means you can just take your time, research everything, do easy missions over and over and after a while you're assaulting the first alien base with a completely decked out squad with Plasma weaponry, Titan armor and max level on all 6 of your troops. And since you didn't assault the alien base until then that means you never saw a hint of Ethereals or Sectoid Commanders. And the rest of the campaign just becomes tedious busywork as there's no researches of note left and no cool things to do beside getting one of your squad to max level psionic.
What the game needs is for aliens to be an actual threat that can bite you if you take too long before you act.