A protagonist's intelligence is limited to that of the author?

agreed ... even in acting it's easier to play stupid then to play highly smart, unless you aren't playing 

An author making changes as they see fit but to when it contradicts story or character continuity is something they should be prepared to be criticized about! 

To write a 'smart character', the author only needs to make the character know more than the other characters. Since the author knows the plot, all he needs to do is make the character able to piece things together based on already presented facts. That's not deus ex machina. Arthur Conan Doyle was not a genius by any stretch of imagination, but he knows how to write detective fiction that we thought Sherlock Holmes was a smart man, when we at the same time could've come to the same conclusion as Sherlock Holmes if we have only pieced things together earlier instead of smacking our foreheads thinking, "Why didn't I think of that before?"

That being said, stories that normally has 'genius characters' shoved to our faces from the description alone are usually quite dumb. You would wonder why this character is called a 'genius' when all he is, is a Mary Sue. Ai-chan has met some real geniuses and these characters are certainly not it. Nothing more than the author's self insert.