You're correct that the modern day storyline is the glue that holds everything together but the problem is not the content but the dramatic execution: there is just no emotional connection to the characters and the stakes in the modern day.
You obviously enjoy the intellectual challenge of figuring out the puzzle of the meta-narrative but that level of engagement just doesn't happen with the mass audience these games are being made for... most people want the emotional investment as well. It's obvious that the writing room knows what they're doing but game director after game director has paired down the modern day segments to the point where we only have perfunctory exposition, some very broad strokes characterisation, almost no dramatic tension and all pertinent information hidden in optional documents/emails.
So yes, Layla is key to the whole AC universe but the way she's been presented and how players interact with her just doesn't resonate... I don't fault players for the sentiment that Ubi should drop modern day altogether, it's a problem of their own making and I'd like to see the devs do better.
IMO, it's part of a larger design shift in Ubisoft's games. In the old days, Ubisoft had characters like Desmond, Ezio, Jade, Jason Brody. Strongly defined characters who are developed through cutscenes and a linear story. They don't do that anymore. Far Cry 5's Rook is a silent cipher. Kassanda in AC: Odyssey is a great character, but she has essentially minutes of traditional linear story development spread over a 20-50 hour long game. Anything that doesn't fit into the non-linear "explore the world, meet characters, solve their problems" formula is pushed into the background. It's very important and Ubisoft take this world building very seriously, but they're not going to lock you in a room and feed you exposition. Or if they do lock you in a room it'll be for under a minute. Ubisoft are creating games for the kind of people who ragequit Half-Life 2 because it made them stand in a room and listen to Barney and Dr Kleiner talk. Ubisoft have tried to broaden the appeal of their games by making them gameplay focused above all else. I'd argue this has been effective to some degree, but it has alienated older Ubisoft fans who loved the likes of AC2, and it has caused these newer AC fans to resent legacy story stuff. There are some people who hate cutscenes in the Far Cry games. They just want to shoot things. They're not interested in characters, story, plotting, world building, or any of that stuff. And Ubisoft cultivated this mentality intentionally. But they wanna have their cake and eat it, too. They want to have their 2deep4u plots with hidden meta layers and clever bits. But they also want to create games that appeal to people who hate storytelling. And obviously you can't please everyone all the time.
Some people complain that, "Oh, if only Ubisoft hired better writers they'd create emotionally engaging narratives like <insert other game series here>", but the problem is Ubisoft don't want to create those types of stories because those kind of stories almost invariable involve telling the player a story, and Ubisoft's lead creative has a "Don't tell me a story" ethos. The disgruntlement some have with Layla's storytelling (and I'll admit I wish it was flashed out and advancing faster) is actually tied to Ubisoft's direction as a company. Remember when Assassin's Creed games had set pieces in them? Like, actual set pieces? Ubisoft have moved away from all of that stuff in favor of non-linear exploration and emergent game design. Yea, they have cutscenes. Yea, they have SOME set pieces, albeit really loosely scripted ones. But they're few and far between.
If Ubisoft were making a game like The Last of Us 2, it would be an open world game where Ellie spends 40+ hours wandering around solving crimes and shit. There would be a bit of personal drama thrown in there, but the linear story people love in Naughty Dog games would be pared back to literally minutes. Slow walking sections? "Burn it with fire!" screams the Ubisoft executive. Those long cutscenes, those long conversations, those long sections where you can't do whatever you want -- those would be pared down and removed. AC: Odyssey and The Witcher 3 are kinda interesting to compare in the sense that while AC: Odyssey is based on TW3, it's created with a mindset that a game like TW3 is boring because the cutscenes go on and on. Also boring because it tells you a story instead of having thousands of stories you can tell yourself. Yet those long cutscenes and character moments that arise from linear plotting and traditional pacing are why a lot of fans like TW3.
Just look at how drastically the approach to storytelling has shifted between Beyond Good & Evil and Beyond Good & Evil 2.
