It sounds like you're doing most things "right" for better FE. How long are most of your trips? That's about the only thing that jumps to my mind as possibly lowering your FE. If most of your trips are short (5-10 mins) then you're not getting as much benefit as you could if you had longer trips.

I can't say that I've noticed any "choppy" feeling as the battery kicks in and out ... when I'm stopped at a light and the ICE engine shuts down, I can usually feel that vibrarion but unless I'm paying a lot of attention, I don't notice this when driving generally.