I think this makes a good point too in that this all assumes Bavarian stays as Autonomy! I personally don’t really think any of the Intents have particularly positive or negative connotation cuz I’ve always thought that one of the big ideas B Sands is exploring with is comparing different ambiguous traits and how they manifest in different situations and what that creates! (Miles vs. Kelsier, Gavilar vs. Dalinar, Szeth vs. Nale, etc.) I think and hope that one of the things that he’s trying to show is that nothing (or very little) is the correct path of action in every situation so it’s down to an individual introspection and understanding of values, situation, responsibilities, morals, etc..
All that being said the point was: if Bavadin stays Autonomy, you’re right it seems somewhat out of character for them to become the big bad, but that assumes that Bavadin stays Autonomy! If someone who’s like super anti-coalition, anti-nation, anti-agreement, anti-interaction between humans becomes Autonomy then maybe I can see them being opposed at the end (cuz I know Brands said it was gonna be about inter-culture interaction and conflict) but that feels a little like a reach. I always thought the big bad was some force anti-Adonalsium I thought that was talked about in a WoB somewhere.