Not to be a smartass, but the odds of Trevor (Lilly's father, Shannon's first husband) being Becca's father (at least biologically) are rather slim. Theoretically it's possible, but graduating college in a month, settling into a new environment, and finding a temp job is a tight deadline.
I mean it's entirely possible that CNG just screwed up with the timeline and Trevor really is her father, but the question remains: if she really did get pregnant by Trevor with Becca, why did her parents send her off to live with her aunt? And since Frank obviously didn't know either, it's going to be something that's an uncomfortable family secret. And I guess a teen pregnancy in 1996 would be something like that.
As for Becca as Shannon 2.0, I think that would have been Lilly. Becca does have a manipulative side, as does her mother, but I think that's where the similarities end. Becca is much more intelligent than her mother and knows when it's wise to make a move. Lilly, on the other hand, has more in common with Shannon for me: they both have quite a temper with a damn thin fuse. And a damn intimidating "if looks could kill" look. And even though with her it's more a product of her childhood trauma of losing her father, I'd say the fact that she's had some relationships where it's more physical is a classic Shannon thing too.
And I mean, Becca said it herself at the beginning: If Frank and Lilly don't get emotionally closer, it's going to come down to her getting knocked up by some jerk and getting dumped. And who did that happen to? Shannon (and Jess, too). We know next to nothing about Shannon's childhood, but I think it's easy to assume she was an only child. She's kind of the cliché of the only child. Lilly initially only had Becca (who was able to balance Lilly out to some extent) but I think the important point that ensured that Lilly didn't become like her mother was Abby, but also Frank. Even if she didn't always listen to Frank, the rules that Frank helped to impose were enforced by Abby (who was a good friend to Lilly and looked after her when they were out) and Becca, who hammered it into them. When it finally clicked with Lilly, it was the last stone that needed to be laid so that she wouldn't go down her mother's toxic path and she could develop a healthier personality.
I don't want to devalue the fact that Frank was also an important person for Becca's development, on the contrary, but if either of them was in danger of becoming a new Shannon, it was Lilly.
In contrast, I like to ask myself: What if Shannon had died instead of Jess and Becca and Lilly had ended up with Frank and Jess? I think Lilly and Abby would have become good friends here too, and even though it wouldn't necessarily be easy for Jess, since they both resemble their mother, I think she would have been a better mother to them.