[@The Harbinger of Ferocity] I'm personally not a fan of 3.5e... can't stand skill progression, and a few other details that just make it very frustrating to play. PF fixed most of those issues, but that version is miles harder than 5e to pick up and play. 5e, in my opinion, is much easier to use for a beginner's style game.

That said, I'm not sure what you plan for a 3.5e story, but I can’t think of anything that 5e's mechanics would preclude in terms of story. A 5e campaign can be just as dark and gritty as any 3.5e game. A few quick tweaks to keep players on edge: treat long rests like short rests in terms of regaining hp, and reduce the hit die recovered. For short rests, reduce the hp gained to maybe a single hit dice. On death saves, increase the DC for successive KOs between rests. Perhaps stack this increase with the number of times someone has died and been raised (so one death increases the dc of all death saves to 11, and it goes up grom there). Just those two changes significantly alter the difficulty of the game, and force characters to be smarter about using health as a resource. In terms of magic, I've never played a true low-magic game that put any restrictions on PC abilities beyond the rules. Unless you're planning that, 5e mechanics should suffice. Otherwise, you would have to rewrite neatly every class, but that's the same with 3.5 too.

In short, anything you plan in PF or 3.5e can be done in 5e, with maybe a few rule tweaks. But I find tweaking 5e to be simpler than tweaking the older versions.