The thing about story-telling, is that it's considered poor form/bad writing to add focus points to story that don't pertain directly to narrative being told -
that is to say, for example, if you're writing a detective novel, you don't write a paragraph focusing on an object that is of no real relevance, that for instance draws focus away from important clues such as to who the culprit is, or what the murder weapon was.
In relation to FFVII more directly though - a compilation tie-in like the compilation Buster Sword hiding underneath the guard of the original sword is a tie-in that is self-explanatory even to people who didn't play Crisis Core, because the reveal can be directly tied to flash-backs of Zack wielding the compilation version upon his death.
Having the camera shift to an apple in the Nibelheim reactor on the other hand would be bad writing, because it does no such thing.
As long as Genesis as a character does not appear in the remake, nor his scene with the apple, the appearance of the apple itself becomes an unanswered question in the minds of everyone who takes notice of it who didn't play CC, and depending on how dominant that object becomes in the scene, that could be a lot of people - and that would be bad writing.
Now, bad writing isn't exactly beyond Nojima, or anyone else at SE. Games also have a tendency to add Easter eggs without much concern for how it impacts the "quality" of the writing as a whole - after all, games are games, not novels.
It's a relatively minor issue generally speaking.
That being said, I think there are much better ways to make tie-ins to the compilation (such as the Buster Sword thing) and I'm not sure how much purpose it would serve to forcefully try to make tie-ins to things in the compilation that has/had no bearing on the original plot.
I mean, CC is Zack's story - not Cloud's. Genesis and Angeal are not important for the plot of FFVII (after all, they were added later for the sake of fleshing out Zack's story - not for the sake of filling holes in FFVII's story).
Are there ways to tie them into the plot of FFVII? Sure, but if they're going that route I'd prefer if they did it in a more meaningful way than put apples in reactors, or a file you may or may not read in the Shinra HQ data-base where the only purpose of the tie-in becomes a *wink-wink-nudge-nudge* to people who played a game that's only available as a physical copy for PSP.
And, based on Nomura's statement to Famitsu about the lack of clarity in the compilation, I do think they intend on making tie-ins that attribute to a stand-alone story that can be easily followed by both old fans and new alike - not a story that spends time and effort making obscure winks at people familiar with the compilation.
As for the weapons fighting -
It's not like gaming has moved beyond hitting large monsters in the feet repeatedly until they die (Xenoblade series), so it's not like that's a real problem regardless of how they choose to handle it.
. No FF game ever had anything like that since then. IIRC
