Actually the tentacle fight with the WE is given precedence through out the film. On Krypton we see the Kryptonian's use of their "liquid metal" tech for a variety of things, in computer read outs/displays and in their levatating robots, like Kelex (the robot that assists Jor-el) and Kelor (the robot with Lara when Krypton implodes). Later in the ancient scoutship we see a sentry robot use a "liquid metal" tendril to try and subdue Clark. There they establish that even a small version of this tech can at least stymie a super powered Kryptonian and at least cause one to react in pain. It also clearly establishes that this tech was indeed used by the Kryptonians as a defense measure. The World Engine was just a super sized version of a technology established in the earlier part of the film and continually built upon. So, no, the WE tentacle fight does not just come out of no where. In fact when the trailers first hit people were speculating wildly as to what the tentacle shown in the trailers might allude to. Was it Brainiac? Some weapon of Zod's? So it should not have actually surprised anyone. It was established as an element in the film even before it came out and was noticed enough to have sent posters on this forum's imaginations racing.
Now as to why the WE has defense system of some kind? Is this actually some kind of gigantic stretch? MOS is pretty much establishing the classic scifi side of this nascent DCCU it would seem to me. If you want to assume that in such a fictional universe there are NO versions of the various antagonistic alien races and space faring societies that are present in the comics that's your right. But I doubt a film that's the cornerstone of an expansive DC UNIVERSE is only supposed to have TWO humanoid races. The film's writer himself establishes that in the tie-in comic he wrote, as ruling council members mention "the savage Thanagarians" which are of course the people of Shayer Thal and Katar Hol, aka HAWKMAN and HAWKWOMAN, humanoid aliens. If you don't want to accept that because it's a comic tie-in, ok, but it being written by the film's writer gives it extra weight to my eyes. And again, it seems inevitable that other alien races, not all of them good natured are going to come to light in this new DCCU, so, yeah, Kryptonian's outfitting the WE seems pretty damned reasonable and not some grand leap. Neither would Zod adding a defense system to the WE, considering his nature or his ultimate plan for Earth. Really the question of why the WE had something to defend itself after all that was seen in the film or what could easily be intuitted by an audience member comes across to me as nitpicking for the sake of it.
As for the suit? This seems a matter of taste to me. If you felt the moment had no gravitas or what have you, well that is certainly your right to have as an opinion, or to share with this article you read as the case is. Seeing as it makes it's appearance right at the end of Jor-el's revelations to Clark about his origin and then bestows his people's native clothing on him it would seem to me it has more than enough dramatic significance. Again that's just my opinion. Whether the Jor-el A.I. was aware once uploaded into the scoutship that it contained a suit for a member of the House of El or if he had the suit created once installed seems kind of besides the point to me.
Now as to the question as to why Clark seeks out advice from a human religious authority? Well, for myself it's plain Goyer and Snyder are presenting Superman as someone whose sense of self starts with being a midwestern farmer. Despite searching for answers to his origins, he is clearly attached to, molded and raised in the human culture of the American state of Kansas. He plainly states so at film's end. This was not like Chris Reeve's Superman that undertook many years of tutelage in the Fortress of Solitude with that film's version of the Jor-el A.I., one which we see he seems to even have developed an emotional attachement to. No here, however long Clark spends with Jor-el whether weeks or little over a month before he returns to see Ma Kent, it appears Clark would not naturally go running to Jor-el for counsel or advice. Having established that Clark has some kind of faith when he's younger ("Did GOD do this to me?!")
it doesn't come off as odd at all that he'd seek answers/counsel from a religious authority.
Now the idea that he should have gone to the scoutship does have some validity to it, I can't deny that. But between Clark clearly wrestling with the implications his whole life of what revealing his existence would mean and Zod's 24 hour deadline he could be granted a mulligan here at least. It also seems to me that this complaint is pretty much aping the criticism from the HOW IT SHOULD HAVE ENDED MOS installment. Just one problem there though... the HISHE solution actually wouldn't work in the context of what actually IS established in the film. In the HISHE for MOS the HISHE crew seem to think all Superman would have to do is fly the ship that brought him to the planet up to the BLACK ZERO, activate it's Phantom Drive and problem solved, right? Not really, since in order for that to work the BZ's Phantom Drives also have to be active, something Zod is clearly shown to do only after releasing the WE and taking a position over Metropolis. In other words I don't know what Superman would have accomplished with such a tactic, but it would not have created a singularity sucking the BZ and it's crew back to the Phantom Zone. So, sorry HISHE guys. I love your work but this time I'd say they actually let their dislike of a film cloud their judgement as to what realistically would happen if a film adopted their solution to a given situation.