I'd say the fact most people missed the fact that the game hints to the orphanage scene is pretty much the opposite of subtitly done well. I'll give you Laguna but I don't feel the game was really subtle about that one. Actually I'd say Laguna and Squall's familial relationship was probably done well but the problem with these compared to the Griever/R=U theory you are proposing is that the game doesn't leave any questions unanswered concerning the Squall/Laguna twist. Ellone mentions that Raine had a child that Laguna never met, Squall is always Laguna in the dream sequences, and Kiros practically tells you if you talk to him on the Ragnarok before going to Lunatic Pandora by telling Squall he's lucky he takes after his mother and not his father.
It may not have been directly stated but the evidence is more than just flashing an image. Its not like Squall spends his time focusing on a journal for no reason, and this was the hint that he's tryin to remember his journalist father. The twist has a moment that acts as a definitive conclusion, its never stated outright but the evidence is very obvious when put together. The same happens in VII concerning Zack, which is a person who had been hinted too from the very beginning of the game, and was consistently hinted to throughout the first disc by both Aerith and Tifa. There is also the relationship between Relm and Shadow, which is hinted at strongly by not only subte hints in Thamasa when Relm is first introduced, but downright thrown in the players face thanks to Shadow's dreams and the one Relm has. Not to mention the subtle hint in the FMV opening in Anthologies where an Amano portrait of Relm is quickly flashed over Shadow, before he dices up some ghosts.
The point is, that each subtle twist has a major moment of confirmation. Whether its indirect like Squall/Laguna and Shadow/Relm relationships to the not so subtle one like Zack or Golbez being Cecil's brother. There is always an a-ha moment and R=U really doesn't have one. There is no major subtle hint in the game that truly confirms R=U, its always just another incredible subtle hint that involves major analysis of scenes or minor elements, to even realize its existence. Ultemicia never blurts out something to kind of give her true identity away, no special words for Squall, no major element of her past to explain how she went from being happy and in-love Rinoa to Time Compressed crazy bitch. Rinoa never mentions that Ultemicia's consciousness feels familiar, hell no one even stops to say she kind of looks familiar when they meet her face to face.