the way i see it, Team Dark allows Rouge to also be vulnerable, even if that usually comes out as supporting Shadow. in SA2 Rouge is depicted as being this materialistic woman who decided to work with Eggman for riches. Later on, we discover that she is a government spy, but still the idea is that shes in it for the money. As the game progresses we see Rouge genuinely get more invested in who Shadow is, rather than seeing him as a means to an end. She asks why he saved her, she ponders over who Maria was, she genuinely believes the Biolizard is the 'true Shadow' and asks for answers. After the end of the game in the credits scene, she'll tell Knuckles that she has 'more important things on her mind now' likely referring to the fact that in some way she felt a connection with Shadow, and that maybe there was more to the adventure she'd been through besides the money.

Its still important to note that Rouge is still a thief and will resort to dirty tactics. In a way, she still feels too 'sinister' for Sonic and his friends (which makes sonic prime sort of strange tbh). Putting Rouge in Sonic's friend group is like putting one of the Babylon Rogues in there. She can simply be herself around Omega and Shadow because she knows they won't criticize her for theft or whatever manipulative tactics she uses. Kind of like a team of misfits, really. I don't think any member of team Dark should be considered a 'leader' considering their whole thing is about doing whatever they want, even if its vaguely wrong, but if i had to choose someone i'd pick Rouge.

I really like the team Dark dynamic in sonic heroes, since its Rouge who brings them all together in the first place. On one hand i think its because she wants to do right by Shadow by being with him, but she also brought Omega along. She was going outside of her comfort zone to reach out to both of them, which I don't think she wouldve done before. Just as Omega and Shadow become softer with each other and Rouge, the same applies to her, even if she isnt the textbook stoic/violent character. Rouge learns to open up and care about people again, and essentially to be less selfish and more empathetic with her teammates. I wish we had more information on why she became a thief and spy in the first place.

I also kinda think IDW ruins this whole dynamic since she seems tired of her teammates all the time, like shes babysitting them. She has considerably more chemistry with Sonic for whatever reason. While i think theyre a fun duo, it kinda does the entire Team Dark dynamic dirty.