I suppose it's important to start off with what my opinions are on the first season to provide some appropriate context. To be brutally honest with you, I actually thought Index was slightly better than Railgun. The thing I liked about the ToAruVerse was this whole dark mystery surrounding the Magic world and the darkness of the Science side. Touma didn't nearly come across as annoying to me as he did with most people, and I just loved the priceless comedy associated with his misfortune. Whilst there was plenty to lol about in Railgun (most of the comedy coming from Kuroko), the comedy wasn't as funny to me. Not to mention that the entire main cast is female. I don't know about you, but I need a male character I can connect with. All girl shows like K-On rarely ever work for me. Emotional involvement with the characters is important to me, when watching an anime, and I just can’t get that much from a bunch of girly-girls that I have nothing in common with. Plus Railgun has a lot more 'easy going' feel of things, and I liked Index's "Dark and intense" feel better. So in the end, Railgun was never really going to be better. Not that it wasn't much worse. I really love the ToAruVerse but I gave Index a 7, because of its many flaws and I stand by that. Railgun doesn’t deserve anything less than a 7, though as well. So I guess Railgun is merely just a somewhat weaker 7.
The Level Upper storyline was great and all, but it only consisted of a few episodes and relied on a lot of single episodes at the beginning to set the scene. The arcs that followed afterwards weren't that great and were average at best, except for the last episode which I think ended strongly, despite some clichés. In fact, I'd say that Railgun was considerably worse than Index, if Saten wasn't in the the show. As it stands though, Saten is what made me consider the Railgun series more than average, although she alone couldn't really make it better than Index because she was only truly the focus for a handful of episodes.
With that in mind, the context when going into the second season of Railgun was like this: It's an expanded version of the Sisters arc which I liked in Index. However, simply being an expanded version of an Index arc means it could never truly surpass Index because Index has a lot more going for it. So my feeling was that it would simply be a side story of Index, rather than something in its own right, like Saten's story was.
As for Saten's involvement, I already knew she had no involvement in the Railgun manga telling of the Sisters arc so I wasn't expecting much from her here. Since I had no idea how different the Sisters arc in Railgun would be to the Sisters arc in Index, my initial hopes were that she'd be fully integrated into the Sisters arc and have true relevance. But after considering the whole of the Railgun Sisters arc, I've come to the conclusion that the only way that could possibly end for Saten is a death scene. And that would probably make me give up on life altogether.
Now from a narrative perspective, Saten, Uiharu and Kuroko deserve to be included and fully integrated in the Sisters arc because they're Misaka's friends and the Railgun anime has built up the "four member crime busting team" as its main theme. It's main theme: It's what Railgun was all about. It may have been a crappy and cliché theme but it was sincere and heartfelt. To disregard that is to create a massive inconsistency in its narrative.
However, the reality is that Saten was never meant to be a part of the Sisters arc, and the only way to have Saten involved and stay alive at the end of the arc would be to fundamentally change the story and have it completely contradict the Index version. As much as I like Saten, the fact of that the matter is that twisting events that then contradicts established canon would feel like a massive retcon. Even worse, if there's no sign that the author is okay with it then that essentially means the sincerity of the source material is being jeopardised by the person adapting it. If the person adapting the story isn't being faithful to the original story then that means the original isn't being treated with respect. And if the original isn't being treated with respect, then that shows to me that there's a lack of sincerity involved in the storytelling. The best adaptations are those that have a great love of the original story because that love ends up showing in the adaptation itself.
Ultimately it's about making the best out of a bad situation, and I think when it comes down to it, it's more important to remain true to the original even if it does create a narrative inconsistency. Nagai did at least make an effort to show that Saten and the others were in the background and that too has its pros and cons. The pro is that it lessens the narrative inconsistency somewhat, as the show does not completely disregard them altogether. The con, however, is that it makes the giant differences in tone and narrative all that more apparent. The obvious example is Saten who, as you've correctly pointed out, doesn't deserve to be degraded as a background character and that makes it all the more apparent. Once again, this is about picking the least bad choice and I think ultimately Nagai made the right decision.
Thankfully, I was able to overlook these flaws for the most part because the Railgun Sisters arc was just so damn awesome and much better than I had anticipated. I didn't think it could surpass Index but it actually did. The Sisters are far more likeable and sympathetic, and their frequent tragic moments can be really gut wrenching. There's so much more expansion into the Sisters' and Misaka's characters that's well worth the watch. As a whole I was far more emotionally involved in the Railgun version of the Sisters arc than the Index version, and I'd heavily recommend watching it.
As for what happens after the Sisters arc, I don't want to see the Sisters treated the same way as Misaka's friends and want them to remain the focus of the show. This season has been all about the Sisters, so I hoped that the show would remain consistent to that narrative and make the remainder of the season stick to focusing on them. It would've probably been better if Misaka's friends remain in the background because for me they've been far too detached to this story to be convincingly reintroduced as part of the main cast. The whole "four member squad" was dealt a very significant blow in the Sisters arc and I just think it rings a bit hollow now. I suppose they could try and build it back up again but to be truth it just feels like they’re pretended there wasn’t any blow to begin with. Plus I have a fear that their reintroduction will make the story shift into the more light-hearted direction we saw last season, and the content there wasn't much to brag about (besides Saten obviously). It would make the story seemed like it climaxed too early. However, if there is a way to have this new arc be about the Sisters, whilst remaining just as dark as the Sisters arc AND include Misaka's friends, then that could potentially fix the damage that the Sisters arc caused. I'm not optimistic though.
At this point you're probably pissed at me with some of the things I've said. Well so be it: I love Saten but I love her reasonably. It's not nice to see her degraded as a background character but I definitely don't want to see her character being used to jeopardize the sincerity of the story. In my eyes, that would be an even worse use of her character.
As for Saten's fashion, she looks awesome all the time.
I never fail to love every new outfit she has.