I am getting the feeling that Kishi made this part of the story as an afterthought after the first part, i.e. Zabuza-Haku part.

First, how was the body-disposal squad of Konoha not able to retrieve Obito's corpse, or did they lie, since Kakashi appears so surprised to see that Obito is alive? This recent chapter showed us that the body disposal squad is important since the Blood Mist ninjas still want to retrieve Rin's body because of the important intel they could cull from it.

Second, Kakashi not knowing he had MS for almost ten years seems really lame.

Third, where the hell is THE Yellow Flash when he is needed?
He conveniently disappears this second time and another team 7 member dies.

Fourth, the Hashirama-DNA infused suit is also very convenient since we haven't seen Hashirama himsef use this jutsu of passing through walls, earth, and people. If he is the origin of this jutsu that made Obito 'invincible' then Hashirama should have been invincible, too.