Great episode. It's hard to overlook the similarities of John being promoted to chief engineer to Geordi's sudden promotion to that position in TNG. Although, I suppose Chekov's sudden promotion to chief engineer in STID is an equally valid comparison. Only here, they actually take the time to explain how someone can go from a bridge post associated with flight operations to the head of engineering, over everyone else down there who arguably has more seniority in that particular job. That's certainly a lot more interesting a direction to take this storyline.
Although, now that John's in engineering, I'm assuming the navigator position is likely no longer a speaking role? I guess I can kind of understand, Gordon and John overlapped each other often enough throughout the season anyway. But on the other hand, it's kind of the frustration I've had with the Abrams Trek movies in that it doesn't seem anyone really understand the role of a navigator other than being a sort of "co-pilot." Aside from the warp jump off Titan's atmosphere, nothing in those movies reflected Chekov's expertise as a navigator, and indeed in STID when he was an engineer the replacement navigator wasn't a speaking role.
And while I certainly have no objection to John now being the engineer, it does seem kind of a waste that Chief Newton didn't really do much. Yeah, I know, he was never in the main cast, so they did as much as they had too. Still, if they were going to write the character off in the next episode anyway, I kind of wonder why they didn't just have him be the one they killed off to make Alara question herself in the previous episode. It wouldn't have changed much in the narrative of this episode, John and Gordon could still pull a prank on Yaphit, Kelly would still put a reprimand in their files, during which she discovers John is actually a genius and decides to screen him for the now vacant position of chief engineer.
I loved the Yaphit humour here ("you don't want a gelatinous senior officer on your ship." "No, it's not that. Some of my best friends are gelatinous.") It was interesting to see a more irritable side to him, both in his dealings with John and Ed and even Claire's kids. He had previously been so easy going with everyone, though I suppose what we saw here could be a combination of stress over not getting a promotion he felt he deserved, the idea that the guy who pulled a prank on him could become his boss, and the fact that he likely has no chances with Claire now because of that stuff a few weeks ago.