I would have liked to see the team struggling more to fill in the gap left by Shaw, because she did have skills none of the others had.

You have no idea how much that annoyed me! They did a better job in season 2 portraying why they needed another member with Shaw's skills and they already had Carter helping them out then!

Fusco suddenly getting sniper skillz was annoying! And then Root picking up awesome hand to hand when she didn't before -- like I can headcanon that Shaw taught her etc., etc., but it will still niggle in my head how easily she took down Martine, when in a previous episode we saw Martine take down two men in a bar.

I feel like the show got caught up in how cool it thought Root was and forgot to depower her accordingly when the Machine went silent and she didn't have god mode anymore.

I am just going to point up, because, THIS.