The show did come to a natural plot conclusion because the writers knew they had to end it. Are we convinced if it wasn't cancelled the plot would have been a problem because they are getting older? I'm not at all.
THat is some kind of double standard which is for some reason applied only to Malcolm in the Middle. It is common for sitcoms with teenagers in them for the show to continue long after they arent teenagers anymore. THat 70's show, Married with Children, Cosby show. THat is just off the top of my head in 2 seconfd. Those shows went on and on nobody complained the kids were too old. Danny Masterson is like 30 the last season and still lives in Red's house?