I'll try. I'd have to re-read it to figure out where my favorite parts are, so here are some thoughts on the overall story.
1) The story is very character-driven, like much of the JMS run. Its a personal preference of mine. He writes so much that way, that I think he can get tunnel vision at times where the character interactions kind of become larger and better than the story itself. But in this case I felt the story lived up to the character depictions.
2) Sins Past took an honest and kind of modern approach at the Gwen Stacy character and theorized some new tendencies and vulnerabilities which we had not seen before. Usually she never had problems and is just such a blah, static being. Is the Sins Past approach a bit icky? Yes. But I can deal with icky better than yet another "Gwen is this perfect angel from heaven" story.
3) MJ is really the driver behind the story. Its really about Peter and her relationship, and a secret she has that she has never shared previously and how they deal with that secret as a couple. I felt MJ was treated respectfully. I admit when first reading this I wanted JMS to leave things in doubt as to whether she was a reliable narrator. I still feel that would have been an improvement, just to leave doubt and introduce further story possibilities. But I can understand why he didn't - he thought this whole story would have been retconned away when he wrote it.
4) I respect the boldness of the story and enjoy that it punches me in the gut. Not many stories do that authentically. Its an engaging work, certainly moreso than almost any other Gwen-based story, even Blue which is decent but where I could see where they were going from the very first page. Every single fricking Gwen story is like that except for Spider-Gwen, which isn't even the same character. Sins Past was a real page-turner for me and, while I could have done without some of the imagery, the pseudo-realism of Deodato was a gut punch that works in context. I mean if you are going there anyhow, I respect a writer going all the way and embracing where he is headed.
There's probably more. The twins actually being around, I'm kind of on the fence about. Feel like it would have been better to have killed them off at the end of the story.