I mean, I don't disagree, but the line between a quality graphical update and a shit one is sometimes thin, especially for developers who also have to take costs into account. I've heard a lot of stories about supposedly updated DVDs looking worse than their predecessors (an extreme example is the Star Wars original trilogy remasters, although George Lucas' insanity plays a role there). Less glaringly, I remember hearing about how the original Suspiria looks absolutely awful on DVD despite being a beautiful movie.
I'm sure the people who made the FFVI iPhone port thought it looked good, when it looks like ass. The mentality is probably usually something like 'we want to attract as many new viewers/players as possible while also offering enough of an excuse for older fans to buy the product again'.