Though I ultimately agree with the two of you about how there should have been more substance between Riki and Saya, I feel as though there are some points you’re being a bit unreasonable on.
First and foremost, Saya and Kyousuke are only "Mary Sue"s from Riki’s perspective. Riki has a bad habit of aggrandising those around him, especially those who made strong first impressions. Just as we see the weakness of characters like Kyousuke and Kengo in Refrain, you have to look at Replay and Aya’s backstory to get a more even-handed and human view of her.
Second, the Suspension Bridge Effect. There’s no way the situation going on would have no effect on Riki’s mental state. He was scared and under stress, especially for those first few days. During that time, Saya was his only companion - the only person he could trust - which in of itself fulfils the conditions for the Suspension Bridge Effect. Not to mention, from his perspective, she would likely have seemed like a saviour. Not only would it seem like she was “saving” him in a physical sense, but she also rescued him from the “situation”, brightening his mood and relieving him of his stress. We don’t really see much of this in Riki’s POV, though it’s still likely it happened subconsciously. If I were to make a guess, I would say that his initial feelings for her were only due to the SBE, but by the time he got over it, he had developed real feelings for her.
Now to get on with the complaints about the backstory as a single infodump and the general writing of the route. I myself was a bit disillusioned with the route during my second read-through, which is when I started looking at it critically as opposed to the first read-through where I just wanted to enjoy it. That said, I also feel a certain charm from it. It really feels to me like Jun Maeda just wrote exactly what he wanted to write and how he wanted to write it, without worrying about structure or people looking over his shoulder.
Kind of like Song of Saya was for Gen Urobuchi. Insert “Saya” conspiracy theory. Though once again, ‘that said’, I don’t know anything about what was actually going on behind the scenes at the time, that’s just what it felt like to me.