I always felt bad for Sai. He had feelings for Fllay, but she tossed aside their relationship without a second thought for her revenge. Fllay did some really awful things in Seed, but I see her character and motives as distinctly different from Shinn.

In the beginning of the show Fllay had a lot of pride in herself due to her position as a favorite daughter of a powerful politician. When she lost that she felt like she lost everything that was important about her and kind of lost her sense of self. She threw away her pride to get her revenge thinking it didn't matter anymore. Since she couldn't fight herself she cold-bloodedly decided to use a former friend as her weapon. She was more desperate and self-destructive than Shinn is since unlike him she thought she had nothing left to lose. I think if she had the skills to pilot a gundam she would have simply killed every coordinator she could get her hands on, not caring if she was killed in the process.

Shinn, on the other hand, has a very strong sense of self, to the point of arrogance. Yeah, revenge is one of his motives, but not his only motive. He doesn't want to kill every single person in Orb. He would be happy if their government fell apart, but he woudn't sacrifice himself to accomplish it. Shinn also wants power to protect others he cares for and the honor and glory he can get winning battles. He is far from giving up.

I suppose if you compared them you could say that they are both selfish characters, and that could be a disliked characteristic, but I wouldn't say that Shinn is GSD's version of Fllay, they are too different.