That's right, you can either hack off everything you don't need from fceux, or write your own simulator of the fight. Alternatively (an idea AnS posted a few years ago) - put your bot right inside fceux! Actual lua code -> C implementation -> communication to the emu - this pipieline doesn't have as much overhead as, say, lua to C# translation, it still has some. And yeah, go through all the functions it will do during your task and kill the extra overhead.
Warning: When making decisions, I try to collect as much data as possible before actually deciding. I try to abstract away and see the principles behind real world events and people's opinions. I try to generalize them and turn into something clear and reusable. I hate depending on unpredictable and having to make lottery guesses. Any problem can be solved by systems thinking and acting.