Honestly, I still think it's Downfall timeline, all things considered. Not that it's flawless, all things considered, but the issue is more with Link being recognized as a hero during OoT than with Ruto awakening as a sage. Anything that gets Link far enough into OoT to attempt to kick Ganon's butt without rewinding the clock to before it started is going to have Ruto awoken as a sage as far as I'm aware from my basic research on the franchise and watching discussions.
. . .Actually, what timeline WOULD OoT be recognized as a hero in? Child wound back time and never did anything in the first place that anyone in Hyrule would know aside from squeal, dying in regret. Adult he vanishes and doesn't show up in it's hour of need and the world had to drown as a result, although the sages were still recognized. Downfall he just flat out died. OoT Link has a. . .bad track record.
Of course, Child is both the timeline least likely to give Link recognition due to aforementioned regrets and the least likely to have Ruto awake since there was never a reason for her to at the time. . .
As Hyrule climbed out of medieval stasis 10,000 years ago and had all previous games BEFORE then and the map for an open world game was almost certainly redrawn, I don't really pay attention to geographical evidence for ANY of the timelines in my observations. For me, the buildings are handwaved in my head as being as cyclic as the reincarnation of the hero and princess and anything else breaks my head that little bit harder.
That said I'm more team "There's a dozen other things I find more fun to overanalyze in a video game than the order the games take place in." I find pointing out openings for alternate possibilities from whatever the consensus in the room is interesting, but left to my own devices I'd probably be more interested in contemplating the events of 100 and 10,000 years ago and what happens from now on rather than the older Zelda timeline.
. . .Maybe there's a fourth timeline. Maybe Link won, then Zelda offered to send Link back and then Link was like, "Nah I can manage without those seven years of my life, what if something worse happens if I'm not here?" Then Link pairs up with his ship of choice and everyone lives happily ever after and society moves on until someone gets the stupid idea to force everyone back into medieval stasis. Hyrule is there, Link wins and is a recognized hero, Ruto is awoken, etc.