It's been quite some time since I've used this system and my memory is a little fuzzy. Despite my earlier ravings on it, we ended up deeply dissatisfied with the system. Seeing that you're shouting out for it, I'll try and remember/dredge up our issues.
The big issue is, I think, the tension between resolving conflicts using capabilities and resolving using themes. Themes are a win-button. You've just been fighting an epic battle back-and-forth and it comes to the end - you've lost. So you use a twist and nullify the loss.
Thus, a sufficiently motivated player will never lose. Unless you want to lose, there is no reason why you should. This doesn't work if you consider the player's role as being the character's advocate. I want to fight tooth and nail for my character to achieve their goals. SA lets me to it trivially, and while it's awesome for a while (for the player - not awesome for the GM), eventually you realise that because your character has never seriously been challenged, they haven't had very much opportunity to grow. I had to give up using twists to advocate for my character because it was making the game bland.
In theory, a complication should balance this out. It doesn't. It generally adds a new story element and the player will go on to win whatever issue that brings up in the same manner. Also, the handling time necessary for a player to think up a good complication is rather long.
After a while I figured out what people were talking about themes being 'anti-flags' was about - themes don't help create situations involving what the theme is about - they resolve them. Sure, they resolve it in the manner you're interested in, but using a theme signifies the end of the bit of story that was interesting and generally sucks out the tension from what should be the meat of the story.
Another major point of contention was what happens when you win/lose a social conflict. We ran into a lot of weird outcomes where according to the rules, my character had just been convinced to a viewpoint that was utterly at odds with everything that had previously been established about that character. Social conflicts work really well for the most part, but not when the opposition is pushing for you to (say) betray everything you believe in (and are not controlling your mind with technology) after a fairly low-key conversation. There could especially be a problem here when what's at stake changes as the conflict/discussion goes on.
Conflicts can also go on for way too long. We ended up scrapping double reserve for professions because it dragged out one conflict for forever. Nesting conflicts can sometimes give this effect as well.
There were other issues, but some of them were caused by our rule hacks fixing other issues, so probably outside the scope. We did have to come up with a lot of hacks and just decide on what some of the ambiguous stuff meant (there are way way not enough examples in the rulebook).
The big thing is twists though - it took me a very long time to realise how the fun was being sabotaged by too much success. It's insidious, and I don't think you'd notice it in a short game. Themes are something that we all really liked the concept of … but they just don't do what they should for them to be satisfying.