The way I see it is that unless a variable name shadows a very commonly used matlab function (sum, size, max, etc.), I don't think it's worth pointing out. The problem is that, due the lack of namespaces, you don't stand a fighting chance of knowing if a name you use doesn't shadow a function in one of matlab's many toolboxes.
In code that obviously doesn't deal with complex numbers, I certainly don't think it's worth worrying about i. Particularly as, as I said, countless examples in books and on the web use it as the counter variable. Just look at the wikipedia page on the for loop, i everywhere. Even, with code that deals with complex number, it's only the user's code that can break (I hope that mathwork's own code is resilient) because they explicitly use it as a symbol for the imaginary unit. Therefore, they should already be aware that i means sqrt(-1).
On the other hand, I'd never used i, j, or any single letter variable in any long lasting code. It's probably more beneficial to teach people to use variable names that actually explain their purpose, like fileindex or rownumber, etc. That's certainly what I try to do in my answers (most of the time).