First, the expectation thing. He's using a special case, E(X), and complaining that the more general case doesn't follow the general case. It's like saying "Well the plural of mouse is mice but the plural of house isn't hice!". The general definition of expectation (for a discrete probability) is
E(f(x)) = sum f(x_i)* p(x_i)
If you start with this general definition, both E(X) and E(X^2) are perfectly natural. The author's error of starting with the special case in no way implies an issue with notation.
And how is the fact that Wikipedia is inconsistent between E(X) and E[X] in any way mathematical notation's fault? If you read a novel that starts using ' for quotes and switches to ", that's an issue with the novel (assuming its not stylistic) and not an issue with the typography in general.