Odds are we're going to find out what happened to Rin from Kakashi after this flashback is over. This is technically limited by Obito's memory, so if he never learned the reason it's not going to be in his flashback.
Madara being old as fuck on both ends of a twenty year timeframe isn't inherently plothole-ish. He'd been using the GM to extend his lifespan quite drastically as it was; it's not a far stretch to assume he was just as much of a geezer when he gave the Rinnegan to Nagato as when he met Obito given that he's shown to be using means to extend his lifespan past what it should have been. As for why he looked old way back then, it's again worth remembering that he's connected to the GM. When Nagato tried that shit he went from looking like 20 to looking about 60. I dunno. Doesn't seem bad compared to the horseshit we've seen before.
As for Yahiko not being dead, Nagato is still in "not fucking wheelchair-bound" mode. Ergo, the Hanzo incident hasn't happened yet. It also falls in line with Obito's statements when he was fighting Konan, since he said that he was the one who convinced Yahiko to form Akatsuki. The three Ame orphans are totally alone at this point, no apparent sign of an organized group of allies working with them yet. For the "war should be over by this point" statement with the Mist, we have to remember that we saw A and KB up against Minato during the Third War even though the Lightning country wasn't one of the big three warring nations. There's a definite sense that, even if they're not all-out parts of the battle, all the 5 great villages become entangled in the Great Wars, hence their significance (Leaf and Cloud had a 1 v 1 after Minato's death and that wasn't a "great war").
I'm just saying. We've seen so much worse than this.
I am a leaf on the wind. Watch how I soar.