The reason he isnt in is because in absolute power when they had the 'shoot juanito' edict... thats was there hint that he wasnt going to be into tropico 4 and that they were tired of him... THOSE BASTARDS!!!
I think there are too many Juanito references in Tropico 4 to say they were tied of him, more likely he left because he didn't want to do Tropico anymore are was asking too much.
In one of the missions it was written that there was a man who claimed to be Juanito and that he was the one who assassinated the President of the United States
for 3 1/2 years!?!?! This has been one hell of a drug trip. Well if anyone needs me i will be going to the " everyone loves qaddafi " rall- oh wait nvm